######################################################################################## # Initial Bioinformatics (Quality Control) & Mapping of Sequence Reads to the ‘Alalā Genome: ######################################################################################## ############################# # Index the new genome: ############################# /home/gblanche/apps/bwa/bwa index -p alala_bwa alala-unzipArrow.fasta ############################# # Trim and clean the sample reads with trimmomatic (output is trim): ############################# java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 AC1_S1_L001_R1_001.fastq AC1_S1_L001_R2_001.fastq AC1_S1_L001_R1_001.fastq.paired.trim AC1_S1_L001_R1_001.fastq.unpaired.trim AC1_S1_L001_R2_001.fastq.paired.trim AC1_S1_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 AC2_S2_L001_R1_001.fastq AC2_S2_L001_R2_001.fastq AC2_S2_L001_R1_001.fastq.paired.trim AC2_S2_L001_R1_001.fastq.unpaired.trim AC2_S2_L001_R2_001.fastq.paired.trim AC2_S2_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 CH16_S24_L001_R1_001.fastq CH16_S24_L001_R2_001.fastq CH16_S24_L001_R1_001.fastq.paired.trim CH16_S24_L001_R1_001.fastq.unpaired.trim CH16_S24_L001_R2_001.fastq.paired.trim CH16_S24_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 AC3_S3_L001_R1_001.fastq AC3_S3_L001_R2_001.fastq AC3_S3_L001_R1_001.fastq.paired.trim AC3_S3_L001_R1_001.fastq.unpaired.trim AC3_S3_L001_R2_001.fastq.paired.trim AC3_S3_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 CH1_S9_L001_R1_001.fastq CH1_S9_L001_R2_001.fastq CH1_S9_L001_R1_001.fastq.paired.trim CH1_S9_L001_R1_001.fastq.unpaired.trim CH1_S9_L001_R2_001.fastq.paired.trim CH1_S9_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 AC5_S5_L001_R1_001.fastq AC5_S5_L001_R2_001.fastq AC5_S5_L001_R1_001.fastq.paired.trim AC5_S5_L001_R1_001.fastq.unpaired.trim AC5_S5_L001_R2_001.fastq.paired.trim AC5_S5_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 CH2_S10_L001_R1_001.fastq CH2_S10_L001_R2_001.fastq CH2_S10_L001_R1_001.fastq.paired.trim CH2_S10_L001_R1_001.fastq.unpaired.trim CH2_S10_L001_R2_001.fastq.paired.trim CH2_S10_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 AC6_S6_L001_R1_001.fastq AC6_S6_L001_R2_001.fastq AC6_S6_L001_R1_001.fastq.paired.trim AC6_S6_L001_R1_001.fastq.unpaired.trim AC6_S6_L001_R2_001.fastq.paired.trim AC6_S6_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 CH3_S11_L001_R1_001.fastq CH3_S11_L001_R2_001.fastq CH3_S11_L001_R1_001.fastq.paired.trim CH3_S11_L001_R1_001.fastq.unpaired.trim CH3_S11_L001_R2_001.fastq.paired.trim CH3_S11_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 AC7_S7_L001_R1_001.fastq AC7_S7_L001_R2_001.fastq AC7_S7_L001_R1_001.fastq.paired.trim AC7_S7_L001_R1_001.fastq.unpaired.trim AC7_S7_L001_R2_001.fastq.paired.trim AC7_S7_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 CH4_S12_L001_R1_001.fastq CH4_S12_L001_R2_001.fastq CH4_S12_L001_R1_001.fastq.paired.trim CH4_S12_L001_R1_001.fastq.unpaired.trim CH4_S12_L001_R2_001.fastq.paired.trim CH4_S12_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 AC8_S8_L001_R1_001.fastq AC8_S8_L001_R2_001.fastq AC8_S8_L001_R1_001.fastq.paired.trim AC8_S8_L001_R1_001.fastq.unpaired.trim AC8_S8_L001_R2_001.fastq.paired.trim AC8_S8_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 CH5_S13_L001_R1_001.fastq CH5_S13_L001_R2_001.fastq CH5_S13_L001_R1_001.fastq.paired.trim CH5_S13_L001_R1_001.fastq.unpaired.trim CH5_S13_L001_R2_001.fastq.paired.trim CH5_S13_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 CH10_S18_L001_R1_001.fastq CH10_S18_L001_R2_001.fastq CH10_S18_L001_R1_001.fastq.paired.trim CH10_S18_L001_R1_001.fastq.unpaired.trim CH10_S18_L001_R2_001.fastq.paired.trim CH10_S18_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 CH6_S14_L001_R1_001.fastq CH6_S14_L001_R2_001.fastq CH6_S14_L001_R1_001.fastq.paired.trim CH6_S14_L001_R1_001.fastq.unpaired.trim CH6_S14_L001_R2_001.fastq.paired.trim CH6_S14_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 CH11_S19_L001_R1_001.fastq CH11_S19_L001_R2_001.fastq CH11_S19_L001_R1_001.fastq.paired.trim CH11_S19_L001_R1_001.fastq.unpaired.trim CH11_S19_L001_R2_001.fastq.paired.trim CH11_S19_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 CH7_S15_L001_R1_001.fastq CH7_S15_L001_R2_001.fastq CH7_S15_L001_R1_001.fastq.paired.trim CH7_S15_L001_R1_001.fastq.unpaired.trim CH7_S15_L001_R2_001.fastq.paired.trim CH7_S15_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 CH12_S20_L001_R1_001.fastq CH12_S20_L001_R2_001.fastq CH12_S20_L001_R1_001.fastq.paired.trim CH12_S20_L001_R1_001.fastq.unpaired.trim CH12_S20_L001_R2_001.fastq.paired.trim CH12_S20_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 CH8_S16_L001_R1_001.fastq CH8_S16_L001_R2_001.fastq CH8_S16_L001_R1_001.fastq.paired.trim CH8_S16_L001_R1_001.fastq.unpaired.trim CH8_S16_L001_R2_001.fastq.paired.trim CH8_S16_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 CH14_S22_L001_R1_001.fastq CH14_S22_L001_R2_001.fastq CH14_S22_L001_R1_001.fastq.paired.trim CH14_S22_L001_R1_001.fastq.unpaired.trim CH14_S22_L001_R2_001.fastq.paired.trim CH14_S22_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 AC4_S4_L001_R1_001.fastq AC4_S4_L001_R2_001.fastq AC4_S4_L001_R1_001.fastq.paired.trim AC4_S4_L001_R1_001.fastq.unpaired.trim AC4_S4_L001_R2_001.fastq.paired.trim AC4_S4_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 CH9_S17_L001_R1_001.fastq CH9_S17_L001_R2_001.fastq CH9_S17_L001_R1_001.fastq.paired.trim CH9_S17_L001_R1_001.fastq.unpaired.trim CH9_S17_L001_R2_001.fastq.paired.trim CH9_S17_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 CH13_S21_L001_R1_001.fastq CH13_S21_L001_R2_001.fastq CH13_S21_L001_R1_001.fastq.paired.trim CH13_S21_L001_R1_001.fastq.unpaired.trim CH13_S21_L001_R2_001.fastq.paired.trim CH13_S21_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 CH15_S23_L001_R1_001.fastq CH15_S23_L001_R2_001.fastq CH15_S23_L001_R1_001.fastq.paired.trim CH15_S23_L001_R1_001.fastq.unpaired.trim CH15_S23_L001_R2_001.fastq.paired.trim CH15_S23_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF99-17_S20_L001_R1_001.fastq RCF99-17_S20_L001_R2_001.fastq RCF99-17_S20_L001_R1_001.fastq.paired.trim RCF99-17_S20_L001_R1_001.fastq.unpaired.trim RCF99-17_S20_L001_R2_001.fastq.paired.trim RCF99-17_S20_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF98-53_S19_L001_R1_001.fastq RCF98-53_S19_L001_R2_001.fastq RCF98-53_S19_L001_R1_001.fastq.paired.trim RCF98-53_S19_L001_R1_001.fastq.unpaired.trim RCF98-53_S19_L001_R2_001.fastq.paired.trim RCF98-53_S19_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF98-49_S17_L001_R1_001.fastq RCF98-49_S17_L001_R2_001.fastq RCF98-49_S17_L001_R1_001.fastq.paired.trim RCF98-49_S17_L001_R1_001.fastq.unpaired.trim RCF98-49_S17_L001_R2_001.fastq.paired.trim RCF98-49_S17_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF98-52_S18_L001_R1_001.fastq RCF98-52_S18_L001_R2_001.fastq RCF98-52_S18_L001_R1_001.fastq.paired.trim RCF98-52_S18_L001_R1_001.fastq.unpaired.trim RCF98-52_S18_L001_R2_001.fastq.paired.trim RCF98-52_S18_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF98-48_S16_L001_R1_001.fastq RCF98-48_S16_L001_R2_001.fastq RCF98-48_S16_L001_R1_001.fastq.paired.trim RCF98-48_S16_L001_R1_001.fastq.unpaired.trim RCF98-48_S16_L001_R2_001.fastq.paired.trim RCF98-48_S16_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF98-47_S15_L001_R1_001.fastq RCF98-47_S15_L001_R2_001.fastq RCF98-47_S15_L001_R1_001.fastq.paired.trim RCF98-47_S15_L001_R1_001.fastq.unpaired.trim RCF98-47_S15_L001_R2_001.fastq.paired.trim RCF98-47_S15_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF98-46_S14_L001_R1_001.fastq RCF98-46_S14_L001_R2_001.fastq RCF98-46_S14_L001_R1_001.fastq.paired.trim RCF98-46_S14_L001_R1_001.fastq.unpaired.trim RCF98-46_S14_L001_R2_001.fastq.paired.trim RCF98-46_S14_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF98-45_S23_L001_R1_001.fastq RCF98-45_S23_L001_R2_001.fastq RCF98-45_S23_L001_R1_001.fastq.paired.trim RCF98-45_S23_L001_R1_001.fastq.unpaired.trim RCF98-45_S23_L001_R2_001.fastq.paired.trim RCF98-45_S23_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF98-45_S13_L001_R1_001.fastq RCF98-45_S13_L001_R2_001.fastq RCF98-45_S13_L001_R1_001.fastq.paired.trim RCF98-45_S13_L001_R1_001.fastq.unpaired.trim RCF98-45_S13_L001_R2_001.fastq.paired.trim RCF98-45_S13_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF98-44_S12_L001_R1_001.fastq RCF98-44_S12_L001_R2_001.fastq RCF98-44_S12_L001_R1_001.fastq.paired.trim RCF98-44_S12_L001_R1_001.fastq.unpaired.trim RCF98-44_S12_L001_R2_001.fastq.paired.trim RCF98-44_S12_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF98-43_S22_L001_R1_001.fastq RCF98-43_S22_L001_R2_001.fastq RCF98-43_S22_L001_R1_001.fastq.paired.trim RCF98-43_S22_L001_R1_001.fastq.unpaired.trim RCF98-43_S22_L001_R2_001.fastq.paired.trim RCF98-43_S22_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF98-43_S11_L001_R1_001.fastq RCF98-43_S11_L001_R2_001.fastq RCF98-43_S11_L001_R1_001.fastq.paired.trim RCF98-43_S11_L001_R1_001.fastq.unpaired.tri RCF98-43_S11_L001_R2_001.fastq.paired.trim RCF98-43_S11_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF98-42_S10_L001_R1_001.fastq RCF98-42_S10_L001_R2_001.fastq RCF98-42_S10_L001_R1_001.fastq.paired.trim RCF98-42_S10_L001_R1_001.fastq.unpaired.trim RCF98-42_S10_L001_R2_001.fastq.paired.trim RCF98-42_S10_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF98-16_S9_L001_R1_001.fastq RCF98-16_S9_L001_R2_001.fastq RCF98-16_S9_L001_R1_001.fastq.paired.trim RCF98-16_S9_L001_R1_001.fastq.unpaired.trim RCF98-16_S9_L001_R2_001.fastq.paired.trim RCF98-16_S9_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF98-15_S21_L001_R1_001.fastq RCF98-15_S21_L001_R2_001.fastq RCF98-15_S21_L001_R1_001.fastq.paired.trim RCF98-15_S21_L001_R1_001.fastq.unpaired.trim RCF98-15_S21_L001_R2_001.fastq.paired.trim RCF98-15_S21_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF98-15_S8_L001_R1_001.fastq RCF98-15_S8_L001_R2_001.fastq RCF98-15_S8_L001_R1_001.fastq.paired.trim RCF98-15_S8_L001_R1_001.fastq.unpaired.trim RCF98-15_S8_L001_R2_001.fastq.paired.trim RCF98-15_S8_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF98-13_S6_L001_R1_001.fastq RCF98-13_S6_L001_R2_001.fastq RCF98-13_S6_L001_R1_001.fastq.paired.trim RCF98-13_S6_L001_R1_001.fastq.unpaired.trim RCF98-13_S6_L001_R2_001.fastq.paired.trim RCF98-13_S6_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF98-14_S7_L001_R1_001.fastq RCF98-14_S7_L001_R2_001.fastq RCF98-14_S7_L001_R1_001.fastq.paired.trim RCF98-14_S7_L001_R1_001.fastq.unpaired.trim RCF98-14_S7_L001_R2_001.fastq.paired.trim RCF98-14_S7_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF98-12_S5_L001_R1_001.fastq RCF98-12_S5_L001_R2_001.fastq RCF98-12_S5_L001_R1_001.fastq.paired.trim RCF98-12_S5_L001_R1_001.fastq.unpaired.trim RCF98-12_S5_L001_R2_001.fastq.paired.trim RCF98-12_S5_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF98-11_S4_L001_R1_001.fastq RCF98-11_S4_L001_R2_001.fastq RCF98-11_S4_L001_R1_001.fastq.paired.trim RCF98-11_S4_L001_R1_001.fastq.unpaired.trim RCF98-11_S4_L001_R2_001.fastq.paired.trim RCF98-11_S4_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF98-10_S3_L001_R1_001.fastq RCF98-10_S3_L001_R2_001.fastq RCF98-10_S3_L001_R1_001.fastq.paired.trim RCF98-10_S3_L001_R1_001.fastq.unpaired.trim RCF98-10_S3_L001_R2_001.fastq.paired.trim RCF98-10_S3_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF98-09_S2_L001_R1_001.fastq RCF98-09_S2_L001_R2_001.fastq RCF98-09_S2_L001_R1_001.fastq.paired.trim RCF98-09_S2_L001_R1_001.fastq.unpaired.trim RCF98-09_S2_L001_R2_001.fastq.paired.trim RCF98-09_S2_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 java -jar /home/gblanche/apps/trimmomatic/trimmomatic/trimmomatic.jar PE -phred33 RCF98-08_S1_L001_R1_001.fastq RCF98-08_S1_L001_R2_001.fastq RCF98-08_S1_L001_R1_001.fastq.paired.trim RCF98-08_S1_L001_R1_001.fastq.unpaired.trim RCF98-08_S1_L001_R2_001.fastq.paired.trim RCF98-08_S1_L001_R2_001.fastq.unpaired.trim ILLUMINACLIP:TruSeq3-PE.fas:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:25 ############################# # Mapping to new genome: ############################# for i in *unpaired*trim ; do ~/apps/bwa/bwa mem -t 20 alala_bwa $i > $i.sam done; #Loop did not work for paired reads so made script with all paired ID: ~/apps/bwa/bwa mem -t 20 alala_bwa RCF99-17_S20_L001_R1_001.fastq.paired.trim RCF99-17_S20_L001_R2_001.fastq.paired.trim >RCF99-17_S20_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa RCF98-53_S19_L001_R1_001.fastq.paired.trim RCF98-53_S19_L001_R2_001.fastq.paired.trim >RCF98-53_S19_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa RCF98-49_S17_L001_R1_001.fastq.paired.trim RCF98-49_S17_L001_R2_001.fastq.paired.trim >RCF98-49_S17_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa RCF98-52_S18_L001_R1_001.fastq.paired.trim RCF98-52_S18_L001_R2_001.fastq.paired.trim >RCF98-52_S18_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa RCF98-48_S16_L001_R1_001.fastq.paired.trim RCF98-48_S16_L001_R2_001.fastq.paired.trim >RCF98-48_S16_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa RCF98-47_S15_L001_R1_001.fastq.paired.trim RCF98-47_S15_L001_R2_001.fastq.paired.trim >RCF98-47_S15_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa RCF98-46_S14_L001_R1_001.fastq.paired.trim RCF98-46_S14_L001_R2_001.fastq.paired.trim >RCF98-46_S14_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa RCF98-45_S23_L001_R1_001.fastq.paired.trim RCF98-45_S23_L001_R2_001.fastq.paired.trim >RCF98-45_S23_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa RCF98-45_S13_L001_R1_001.fastq.paired.trim RCF98-45_S13_L001_R2_001.fastq.paired.trim >RCF98-45_S13_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa RCF98-44_S12_L001_R1_001.fastq.paired.trim RCF98-44_S12_L001_R2_001.fastq.paired.trim >RCF98-44_S12_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa RCF98-43_S22_L001_R1_001.fastq.paired.trim RCF98-43_S22_L001_R2_001.fastq.paired.trim >RCF98-43_S22_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa RCF98-43_S11_L001_R1_001.fastq.paired.trim RCF98-43_S11_L001_R2_001.fastq.paired.trim >RCF98-43_S11_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa RCF98-42_S10_L001_R1_001.fastq.paired.trim RCF98-42_S10_L001_R2_001.fastq.paired.trim >RCF98-42_S10_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa RCF98-16_S9_L001_R1_001.fastq.paired.trim RCF98-16_S9_L001_R2_001.fastq.paired.trim >RCF98-16_S9_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa RCF98-15_S21_L001_R1_001.fastq.paired.trim RCF98-15_S21_L001_R2_001.fastq.paired.trim >RCF98-15_S21_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa RCF98-15_S8_L001_R1_001.fastq.paired.trim RCF98-15_S8_L001_R2_001.fastq.paired.trim >RCF98-15_S8_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa RCF98-13_S6_L001_R1_001.fastq.paired.trim RCF98-13_S6_L001_R2_001.fastq.paired.trim >RCF98-13_S6_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa RCF98-14_S7_L001_R1_001.fastq.paired.trim RCF98-14_S7_L001_R2_001.fastq.paired.trim >RCF98-14_S7_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa RCF98-12_S5_L001_R1_001.fastq.paired.trim RCF98-12_S5_L001_R2_001.fastq.paired.trim >RCF98-12_S5_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa RCF98-11_S4_L001_R1_001.fastq.paired.trim RCF98-11_S4_L001_R2_001.fastq.paired.trim >RCF98-11_S4_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa RCF98-10_S3_L001_R1_001.fastq.paired.trim RCF98-10_S3_L001_R2_001.fastq.paired.trim >RCF98-10_S3_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa RCF98-09_S2_L001_R1_001.fastq.paired.trim RCF98-09_S2_L001_R2_001.fastq.paired.trim >RCF98-09_S2_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa RCF98-08_S1_L001_R1_001.fastq.paired.trim RCF98-08_S1_L001_R2_001.fastq.paired.trim >RCF98-08_S1_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa AC1_S1_L001_R1_001.fastq.paired.trim AC1_S1_L001_R2_001.fastq.paired.trim > AC1_S1_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa AC2_S2_L001_R1_001.fastq.paired.trim AC2_S2_L001_R2_001.fastq.paired.trim > AC2_S2_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa CH16_S24_L001_R1_001.fastq.paired.trim CH16_S24_L001_R2_001.fastq.paired.trim > CH16_S24_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa AC3_S3_L001_R1_001.fastq.paired.trim AC3_S3_L001_R2_001.fastq.paired.trim > AC3_S3_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa CH1_S9_L001_R1_001.fastq.paired.trim CH1_S9_L001_R2_001.fastq.paired.trim > CH1_S9_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa AC5_S5_L001_R1_001.fastq.paired.trim AC5_S5_L001_R2_001.fastq.paired.trim > AC5_S5_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa CH2_S10_L001_R1_001.fastq.paired.trim CH2_S10_L001_R2_001.fastq.paired.trim > CH2_S10_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa AC6_S6_L001_R1_001.fastq.paired.trim AC6_S6_L001_R2_001.fastq.paired.trim > AC6_S6_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa CH3_S11_L001_R1_001.fastq.paired.trim CH3_S11_L001_R2_001.fastq.paired.trim > CH3_S11_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa AC7_S7_L001_R1_001.fastq.paired.trim AC7_S7_L001_R2_001.fastq.paired.trim > AC7_S7_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa CH4_S12_L001_R1_001.fastq.paired.trim CH4_S12_L001_R2_001.fastq.paired.trim > CH4_S12_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa AC8_S8_L001_R1_001.fastq.paired.trim AC8_S8_L001_R2_001.fastq.paired.trim > AC8_S8_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa CH5_S13_L001_R1_001.fastq.paired.trim CH5_S13_L001_R2_001.fastq.paired.trim > CH5_S13_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa CH10_S18_L001_R1_001.fastq.paired.trim CH10_S18_L001_R2_001.fastq.paired.trim > CH10_S18_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa CH6_S14_L001_R1_001.fastq.paired.trim CH6_S14_L001_R2_001.fastq.paired.trim > CH6_S14_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa CH11_S19_L001_R1_001.fastq.paired.trim CH11_S19_L001_R2_001.fastq.paired.trim > CH11_S19_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa CH7_S15_L001_R1_001.fastq.paired.trim CH7_S15_L001_R2_001.fastq.paired.trim > CH7_S15_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa CH12_S20_L001_R1_001.fastq.paired.trim CH12_S20_L001_R2_001.fastq.paired.trim > CH12_S20_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa CH8_S16_L001_R1_001.fastq.paired.trim CH8_S16_L001_R2_001.fastq.paired.trim > CH8_S16_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa CH14_S22_L001_R1_001.fastq.paired.trim CH14_S22_L001_R2_001.fastq.paired.trim > CH14_S22_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa AC4_S4_L001_R1_001.fastq.paired.trim AC4_S4_L001_R2_001.fastq.paired.trim > AC4_S4_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa CH9_S17_L001_R1_001.fastq.paired.trim CH9_S17_L001_R2_001.fastq.paired.trim > CH9_S17_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa CH13_S21_L001_R1_001.fastq.paired.trim CH13_S21_L001_R2_001.fastq.paired.trim > CH13_S21_L001_R12_001.fastq.paired.trim.sam ~/apps/bwa/bwa mem -t 20 alala_bwa CH15_S23_L001_R1_001.fastq.paired.trim CH15_S23_L001_R2_001.fastq.paired.trim > CH15_S23_L001_R12_001.fastq.paired.trim.sam ##################################################### # SNP Identification & Filtering ##################################################### #Transform sam into bam files (output is bam): module load bioinfo/samtools/1.2 samtools faidx alala-unzipArrow.fasta for i in *.sam ; do samtools view -bS -o $i.bam $i done; ########################################################## # Change read-group headers in preparation for SNP calls and Sort bam file: # This will combine paired and unpaired (orphan) data ########################################################## java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC1_S1_L001_R12_001.fastq.paired.trim.sam.bam O=AC1_S1_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC1_S1_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC2_S2_L001_R12_001.fastq.paired.trim.sam.bam O=AC2_S2_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC2_S2_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC3_S3_L001_R12_001.fastq.paired.trim.sam.bam O=AC3_S3_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC3_S3_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC4_S4_L001_R12_001.fastq.paired.trim.sam.bam O=AC4_S4_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC4_S4_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC5_S5_L001_R12_001.fastq.paired.trim.sam.bam O=AC5_S5_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC5_S5_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC6_S6_L001_R12_001.fastq.paired.trim.sam.bam O=AC6_S6_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC6_S6_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC7_S7_L001_R12_001.fastq.paired.trim.sam.bam O=AC7_S7_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC7_S7_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC8_S8_L001_R12_001.fastq.paired.trim.sam.bam O=AC8_S8_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC8_S8_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH10_S18_L001_R12_001.fastq.paired.trim.sam.bam O=CH10_S18_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH10_S18_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH11_S19_L001_R12_001.fastq.paired.trim.sam.bam O=CH11_S19_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH11_S19_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH12_S20_L001_R12_001.fastq.paired.trim.sam.bam O=CH12_S20_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH12_S20_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH13_S21_L001_R12_001.fastq.paired.trim.sam.bam O=CH13_S21_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH13_S21_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH14_S22_L001_R12_001.fastq.paired.trim.sam.bam O=CH14_S22_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH14_S22_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH15_S23_L001_R12_001.fastq.paired.trim.sam.bam O=CH15_S23_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH15_S23_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH16_S24_L001_R12_001.fastq.paired.trim.sam.bam O=CH16_S24_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH16_S24_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH1_S9_L001_R12_001.fastq.paired.trim.sam.bam O=CH1_S9_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH1_S9_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH2_S10_L001_R12_001.fastq.paired.trim.sam.bam O=CH2_S10_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH2_S10_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH3_S11_L001_R12_001.fastq.paired.trim.sam.bam O=CH3_S11_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH3_S11_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH4_S12_L001_R12_001.fastq.paired.trim.sam.bam O=CH4_S12_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH4_S12_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH5_S13_L001_R12_001.fastq.paired.trim.sam.bam O=CH5_S13_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH5_S13_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH6_S14_L001_R12_001.fastq.paired.trim.sam.bam O=CH6_S14_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH6_S14_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH7_S15_L001_R12_001.fastq.paired.trim.sam.bam O=CH7_S15_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH7_S15_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH8_S16_L001_R12_001.fastq.paired.trim.sam.bam O=CH8_S16_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH8_S16_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH9_S17_L001_R12_001.fastq.paired.trim.sam.bam O=CH9_S17_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH9_S17_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC1_S1_L001_R1_001.fastq.unpaired.trim.sam.bam O=AC1_S1_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC1_S1_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC1_S1_L001_R2_001.fastq.unpaired.trim.sam.bam O=AC1_S1_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC1_S1_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC2_S2_L001_R1_001.fastq.unpaired.trim.sam.bam O=AC2_S2_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC2_S2_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC2_S2_L001_R2_001.fastq.unpaired.trim.sam.bam O=AC2_S2_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC2_S2_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC3_S3_L001_R1_001.fastq.unpaired.trim.sam.bam O=AC3_S3_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC3_S3_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC3_S3_L001_R2_001.fastq.unpaired.trim.sam.bam O=AC3_S3_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC3_S3_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC4_S4_L001_R1_001.fastq.unpaired.trim.sam.bam O=AC4_S4_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC4_S4_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC4_S4_L001_R2_001.fastq.unpaired.trim.sam.bam O=AC4_S4_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC4_S4_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC5_S5_L001_R1_001.fastq.unpaired.trim.sam.bam O=AC5_S5_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC5_S5_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC5_S5_L001_R2_001.fastq.unpaired.trim.sam.bam O=AC5_S5_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC5_S5_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC6_S6_L001_R1_001.fastq.unpaired.trim.sam.bam O=AC6_S6_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC6_S6_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC6_S6_L001_R2_001.fastq.unpaired.trim.sam.bam O=AC6_S6_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC6_S6_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC7_S7_L001_R1_001.fastq.unpaired.trim.sam.bam O=AC7_S7_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC7_S7_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC7_S7_L001_R2_001.fastq.unpaired.trim.sam.bam O=AC7_S7_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC7_S7_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC8_S8_L001_R1_001.fastq.unpaired.trim.sam.bam O=AC8_S8_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC8_S8_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=AC8_S8_L001_R2_001.fastq.unpaired.trim.sam.bam O=AC8_S8_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=AC8_S8_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH10_S18_L001_R1_001.fastq.unpaired.trim.sam.bam O=CH10_S18_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH10_S18_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH10_S18_L001_R2_001.fastq.unpaired.trim.sam.bam O=CH10_S18_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH10_S18_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH11_S19_L001_R1_001.fastq.unpaired.trim.sam.bam O=CH11_S19_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH11_S19_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH11_S19_L001_R2_001.fastq.unpaired.trim.sam.bam O=CH11_S19_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH11_S19_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH12_S20_L001_R1_001.fastq.unpaired.trim.sam.bam O=CH12_S20_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH12_S20_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH12_S20_L001_R2_001.fastq.unpaired.trim.sam.bam O=CH12_S20_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH12_S20_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH13_S21_L001_R1_001.fastq.unpaired.trim.sam.bam O=CH13_S21_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH13_S21_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH13_S21_L001_R2_001.fastq.unpaired.trim.sam.bam O=CH13_S21_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH13_S21_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH14_S22_L001_R1_001.fastq.unpaired.trim.sam.bam O=CH14_S22_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH14_S22_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH14_S22_L001_R2_001.fastq.unpaired.trim.sam.bam O=CH14_S22_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH14_S22_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH15_S23_L001_R1_001.fastq.unpaired.trim.sam.bam O=CH15_S23_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH15_S23_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH15_S23_L001_R2_001.fastq.unpaired.trim.sam.bam O=CH15_S23_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH15_S23_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH16_S24_L001_R1_001.fastq.unpaired.trim.sam.bam O=CH16_S24_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH16_S24_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH16_S24_L001_R2_001.fastq.unpaired.trim.sam.bam O=CH16_S24_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH16_S24_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH1_S9_L001_R1_001.fastq.unpaired.trim.sam.bam O=CH1_S9_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH1_S9_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH1_S9_L001_R2_001.fastq.unpaired.trim.sam.bam O=CH1_S9_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH1_S9_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH2_S10_L001_R1_001.fastq.unpaired.trim.sam.bam O=CH2_S10_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH2_S10_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH2_S10_L001_R2_001.fastq.unpaired.trim.sam.bam O=CH2_S10_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH2_S10_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH3_S11_L001_R1_001.fastq.unpaired.trim.sam.bam O=CH3_S11_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH3_S11_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH3_S11_L001_R2_001.fastq.unpaired.trim.sam.bam O=CH3_S11_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH3_S11_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH4_S12_L001_R1_001.fastq.unpaired.trim.sam.bam O=CH4_S12_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH4_S12_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH4_S12_L001_R2_001.fastq.unpaired.trim.sam.bam O=CH4_S12_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH4_S12_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH5_S13_L001_R1_001.fastq.unpaired.trim.sam.bam O=CH5_S13_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH5_S13_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH5_S13_L001_R2_001.fastq.unpaired.trim.sam.bam O=CH5_S13_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH5_S13_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH6_S14_L001_R1_001.fastq.unpaired.trim.sam.bam O=CH6_S14_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH6_S14_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH6_S14_L001_R2_001.fastq.unpaired.trim.sam.bam O=CH6_S14_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH6_S14_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH7_S15_L001_R1_001.fastq.unpaired.trim.sam.bam O=CH7_S15_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH7_S15_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH7_S15_L001_R2_001.fastq.unpaired.trim.sam.bam O=CH7_S15_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH7_S15_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH8_S16_L001_R1_001.fastq.unpaired.trim.sam.bam O=CH8_S16_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH8_S16_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH8_S16_L001_R2_001.fastq.unpaired.trim.sam.bam O=CH8_S16_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH8_S16_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH9_S17_L001_R1_001.fastq.unpaired.trim.sam.bam O=CH9_S17_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH9_S17_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=CH9_S17_L001_R2_001.fastq.unpaired.trim.sam.bam O=CH9_S17_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=CH9_S17_L001 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-08_S1_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF98-08_S1_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-08_S1 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-15_S21_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF98-15_S21_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-15_S21 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-45_S23_L001_R12_001.fastq.paired.trim.sam.bam O=RCF98-45_S23_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-45_S23 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-08_S1_L001_R12_001.fastq.paired.trim.sam.bam O=RCF98-08_S1_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-08_S1 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-15_S8_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF98-15_S8_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-15_S8 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-45_S23_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF98-45_S23_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-45_S23 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-08_S1_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF98-08_S1_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-08_S1 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-15_S8_L001_R12_001.fastq.paired.trim.sam.bam O=RCF98-15_S8_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-15_S8 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-46_S14_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF98-46_S14_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-46_S14 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-09_S2_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF98-09_S2_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-09_S2 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-15_S8_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF98-15_S8_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-15_S8 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-46_S14_L001_R12_001.fastq.paired.trim.sam.bam O=RCF98-46_S14_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-46_S14 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-09_S2_L001_R12_001.fastq.paired.trim.sam.bam O=RCF98-09_S2_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-09_S2 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-16_S9_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF98-16_S9_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-16_S9 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-46_S14_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF98-46_S14_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-46_S14 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-09_S2_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF98-09_S2_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-09_S2 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-16_S9_L001_R12_001.fastq.paired.trim.sam.bam O=RCF98-16_S9_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-16_S9 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-47_S15_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF98-47_S15_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-47_S15 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-10_S3_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF98-10_S3_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-10_S3 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-16_S9_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF98-16_S9_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-16_S9 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-47_S15_L001_R12_001.fastq.paired.trim.sam.bam O=RCF98-47_S15_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-47_S15 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-10_S3_L001_R12_001.fastq.paired.trim.sam.bam O=RCF98-10_S3_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-10_S3 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-42_S10_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF98-42_S10_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-42_S10 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-47_S15_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF98-47_S15_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-47_S15 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-10_S3_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF98-10_S3_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-10_S3 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-42_S10_L001_R12_001.fastq.paired.trim.sam.bam O=RCF98-42_S10_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-42_S10 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-48_S16_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF98-48_S16_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-48_S16 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-11_S4_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF98-11_S4_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-11_S4 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-42_S10_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF98-42_S10_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-42_S10 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-48_S16_L001_R12_001.fastq.paired.trim.sam.bam O=RCF98-48_S16_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-48_S16 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-11_S4_L001_R12_001.fastq.paired.trim.sam.bam O=RCF98-11_S4_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-11_S4 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-43_S11_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF98-43_S11_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-43_S11 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-48_S16_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF98-48_S16_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-48_S16 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-11_S4_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF98-11_S4_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-11_S4 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-43_S11_L001_R12_001.fastq.paired.trim.sam.bam O=RCF98-43_S11_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-43_S11 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-49_S17_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF98-49_S17_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-49_S17 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-12_S5_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF98-12_S5_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-12_S5 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-43_S11_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF98-43_S11_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-43_S11 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-49_S17_L001_R12_001.fastq.paired.trim.sam.bam O=RCF98-49_S17_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-49_S17 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-12_S5_L001_R12_001.fastq.paired.trim.sam.bam O=RCF98-12_S5_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-12_S5 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-43_S22_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF98-43_S22_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-43_S22 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-49_S17_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF98-49_S17_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-49_S17 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-12_S5_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF98-12_S5_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-12_S5 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-43_S22_L001_R12_001.fastq.paired.trim.sam.bam O=RCF98-43_S22_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-43_S22 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-52_S18_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF98-52_S18_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-52_S18 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-13_S6_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF98-13_S6_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-13_S6 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-43_S22_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF98-43_S22_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-43_S22 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-52_S18_L001_R12_001.fastq.paired.trim.sam.bam O=RCF98-52_S18_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-52_S18 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-13_S6_L001_R12_001.fastq.paired.trim.sam.bam O=RCF98-13_S6_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-13_S6 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-44_S12_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF98-44_S12_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-44_S12 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-52_S18_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF98-52_S18_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-52_S18 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-13_S6_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF98-13_S6_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-13_S6 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-44_S12_L001_R12_001.fastq.paired.trim.sam.bam O=RCF98-44_S12_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-44_S12 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-53_S19_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF98-53_S19_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-53_S19 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-14_S7_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF98-14_S7_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-14_S7 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-44_S12_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF98-44_S12_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-44_S12 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-53_S19_L001_R12_001.fastq.paired.trim.sam.bam O=RCF98-53_S19_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-53_S19 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-14_S7_L001_R12_001.fastq.paired.trim.sam.bam O=RCF98-14_S7_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-14_S7 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-45_S13_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF98-45_S13_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-45_S13 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-53_S19_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF98-53_S19_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-53_S19 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-14_S7_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF98-14_S7_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-14_S7 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-45_S13_L001_R12_001.fastq.paired.trim.sam.bam O=RCF98-45_S13_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-45_S13 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF99-17_S20_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF99-17_S20_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF99-17_S20 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-15_S21_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF98-15_S21_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-15_S21 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-45_S13_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF98-45_S13_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-45_S13 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF99-17_S20_L001_R12_001.fastq.paired.trim.sam.bam O=RCF99-17_S20_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF99-17_S20 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-15_S21_L001_R12_001.fastq.paired.trim.sam.bam O=RCF98-15_S21_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-15_S21 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF98-45_S23_L001_R1_001.fastq.unpaired.trim.sam.bam O=RCF98-45_S23_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF98-45_S23 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/AddOrReplaceReadGroups.jar I=RCF99-17_S20_L001_R2_001.fastq.unpaired.trim.sam.bam O=RCF99-17_S20_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam SORT_ORDER=coordinate CREATE_INDEX=true RGPL=illumina RGID=184 RGSM=RCF99-17_S20 RGLB=bar RGPU=pu184 VALIDATION_STRINGENCY=LENIENT ############################# #Sort bam files ############################# for i in *rgi.bam; do samtools sort $i $i.srt.bam done; ############################# # Mark duplicates but do not remove them: ############################# #We originally removed duplicates but realized that is reduced the mapping success and coverage. Switched to only marking dup. Jan 12 2018 java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-08_S1_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-08_S1_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-08_S1_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-08_S1_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-08_S1_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-08_S1_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-08_S1_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-08_S1_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-08_S1_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-09_S2_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-09_S2_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-09_S2_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-09_S2_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-09_S2_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-09_S2_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-09_S2_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-09_S2_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-09_S2_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-10_S3_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-10_S3_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-10_S3_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-10_S3_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-10_S3_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-10_S3_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-10_S3_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-10_S3_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-10_S3_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-11_S4_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-11_S4_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-11_S4_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-11_S4_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-11_S4_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-11_S4_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-11_S4_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-11_S4_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-11_S4_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-12_S5_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-12_S5_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-12_S5_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-12_S5_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-12_S5_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-12_S5_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-12_S5_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-12_S5_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-12_S5_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-13_S6_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-13_S6_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-13_S6_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-13_S6_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-13_S6_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-13_S6_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-13_S6_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-13_S6_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-13_S6_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-14_S7_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-14_S7_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-14_S7_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-14_S7_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-14_S7_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-14_S7_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-14_S7_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-14_S7_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-14_S7_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-15_S21_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-15_S21_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-15_S21_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-15_S21_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-15_S21_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-15_S21_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-15_S21_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-15_S21_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-15_S21_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-15_S8_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-15_S8_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-15_S8_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-15_S8_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-15_S8_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-15_S8_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-15_S8_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-15_S8_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-15_S8_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-16_S9_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-16_S9_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-16_S9_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-16_S9_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-16_S9_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-16_S9_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-16_S9_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-16_S9_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-16_S9_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-42_S10_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-42_S10_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-42_S10_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-42_S10_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-42_S10_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-42_S10_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-42_S10_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-42_S10_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-42_S10_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-43_S11_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-43_S11_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-43_S11_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-43_S11_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-43_S11_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-43_S11_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-43_S11_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-43_S11_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-43_S11_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-43_S22_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-43_S22_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-43_S22_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-43_S22_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-43_S22_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-43_S22_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-43_S22_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-43_S22_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-43_S22_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-44_S12_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-44_S12_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-44_S12_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-44_S12_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-44_S12_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-44_S12_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-44_S12_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-44_S12_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-44_S12_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-45_S13_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-45_S13_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-45_S13_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-45_S13_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-45_S13_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-45_S13_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-45_S13_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-45_S13_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-45_S13_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-45_S23_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-45_S23_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-45_S23_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-45_S23_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-45_S23_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-45_S23_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-45_S23_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-45_S23_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-45_S23_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-46_S14_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-46_S14_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-46_S14_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-46_S14_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-46_S14_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-46_S14_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-46_S14_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-46_S14_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-46_S14_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-47_S15_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-47_S15_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-47_S15_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-47_S15_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-47_S15_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-47_S15_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-47_S15_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-47_S15_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-47_S15_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-48_S16_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-48_S16_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-48_S16_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-48_S16_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-48_S16_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-48_S16_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-48_S16_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-48_S16_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-48_S16_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-49_S17_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-49_S17_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-49_S17_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-49_S17_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-49_S17_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-49_S17_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-49_S17_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-49_S17_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-49_S17_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-52_S18_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-52_S18_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-52_S18_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-52_S18_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-52_S18_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-52_S18_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-52_S18_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-52_S18_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-52_S18_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-53_S19_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-53_S19_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-53_S19_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-53_S19_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-53_S19_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-53_S19_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF98-53_S19_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF98-53_S19_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF98-53_S19_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF99-17_S20_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF99-17_S20_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF99-17_S20_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF99-17_S20_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF99-17_S20_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF99-17_S20_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=RCF99-17_S20_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=RCF99-17_S20_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=RCF99-17_S20_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC1_S1_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC1_S1_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC1_S1_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC2_S2_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC2_S2_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC2_S2_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC3_S3_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC3_S3_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC3_S3_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC4_S4_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC4_S4_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC4_S4_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC5_S5_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC5_S5_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC5_S5_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC6_S6_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC6_S6_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC6_S6_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC7_S7_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC7_S7_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC7_S7_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC8_S8_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC8_S8_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC8_S8_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH10_S18_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH10_S18_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH10_S18_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH11_S19_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH11_S19_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH11_S19_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH12_S20_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH12_S20_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH12_S20_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH13_S21_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH13_S21_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH13_S21_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH14_S22_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH14_S22_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH14_S22_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH15_S23_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH15_S23_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH15_S23_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH16_S24_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH16_S24_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH16_S24_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH1_S9_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH1_S9_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH1_S9_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH2_S10_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH2_S10_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH2_S10_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH3_S11_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH3_S11_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH3_S11_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH4_S12_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH4_S12_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH4_S12_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH5_S13_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH5_S13_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH5_S13_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH6_S14_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH6_S14_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH6_S14_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH7_S15_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH7_S15_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH7_S15_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH8_S16_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH8_S16_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH8_S16_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH9_S17_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH9_S17_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH9_S17_L001.R12.001.fastq.paired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC1_S1_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC1_S1_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC1_S1_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC1_S1_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC1_S1_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC1_S1_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC2_S2_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC2_S2_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC2_S2_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC2_S2_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC2_S2_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC2_S2_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC3_S3_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC3_S3_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC3_S3_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC3_S3_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC3_S3_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC3_S3_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC4_S4_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC4_S4_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC4_S4_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC4_S4_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC4_S4_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC4_S4_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC5_S5_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC5_S5_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC5_S5_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC5_S5_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC5_S5_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC5_S5_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC6_S6_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC6_S6_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC6_S6_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC6_S6_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC6_S6_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC6_S6_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC7_S7_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC7_S7_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC7_S7_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC7_S7_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC7_S7_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC7_S7_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC8_S8_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC8_S8_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC8_S8_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=AC8_S8_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=AC8_S8_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=AC8_S8_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH10_S18_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH10_S18_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH10_S18_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH10_S18_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH10_S18_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH10_S18_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH11_S19_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH11_S19_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH11_S19_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH11_S19_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH11_S19_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH11_S19_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH12_S20_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH12_S20_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH12_S20_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH12_S20_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH12_S20_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH12_S20_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH13_S21_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH13_S21_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH13_S21_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH13_S21_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH13_S21_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH13_S21_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH14_S22_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH14_S22_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH14_S22_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH14_S22_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH14_S22_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH14_S22_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH15_S23_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH15_S23_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH15_S23_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH15_S23_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH15_S23_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH15_S23_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH16_S24_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH16_S24_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH16_S24_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH16_S24_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH16_S24_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH16_S24_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH1_S9_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH1_S9_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH1_S9_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH1_S9_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH1_S9_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH1_S9_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH2_S10_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH2_S10_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH2_S10_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH2_S10_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH2_S10_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH2_S10_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH3_S11_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH3_S11_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH3_S11_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH3_S11_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH3_S11_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH3_S11_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH4_S12_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH4_S12_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH4_S12_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH4_S12_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH4_S12_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH4_S12_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH5_S13_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH5_S13_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH5_S13_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH5_S13_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH5_S13_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH5_S13_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH6_S14_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH6_S14_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH6_S14_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH6_S14_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH6_S14_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH6_S14_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH7_S15_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH7_S15_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH7_S15_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH7_S15_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH7_S15_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH7_S15_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH8_S16_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH8_S16_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH8_S16_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH8_S16_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH8_S16_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH8_S16_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH9_S17_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH9_S17_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH9_S17_L001.R1.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False java -Xmx20g -jar /home/gblanche/apps/picard-tools-1.119/MarkDuplicates.jar INPUT=CH9_S17_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam OUTPUT=CH9_S17_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam METRICS_FILE=CH9_S17_L001.R2.001.fastq.unpaired.trim.sam.bam.rgi.bam.bam.mrkdup.txt2 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=False ############################# #Rescale Museum samples with MapDamage: ############################# module load lang/R/3.3.2 module load lang/Python/2.7.10 python mapDamage -i ~/lus/museumDNA/RCF98-08_S1_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-43_S11_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-08_S1_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-43_S22_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-08_S1_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-43_S22_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-09_S2_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-43_S22_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-09_S2_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-44_S12_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-09_S2_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-44_S12_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-10_S3_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-44_S12_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-10_S3_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-45_S13_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-10_S3_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-45_S13_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-11_S4_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-45_S13_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-11_S4_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-45_S23_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-11_S4_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-45_S23_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-12_S5_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-45_S23_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-12_S5_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-46_S14_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-12_S5_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-46_S14_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-13_S6_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-46_S14_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-13_S6_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-47_S15_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-13_S6_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-47_S15_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-14_S7_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-47_S15_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-14_S7_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-48_S16_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-14_S7_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-48_S16_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-15_S21_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-48_S16_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-15_S21_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-49_S17_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-15_S21_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-49_S17_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-15_S8_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-49_S17_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-15_S8_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-52_S18_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-15_S8_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-52_S18_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-16_S9_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-52_S18_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-16_S9_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-53_S19_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-16_S9_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-53_S19_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-42_S10_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-53_S19_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-42_S10_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF99-17_S20_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-42_S10_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF99-17_S20_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-43_S11_L001_R1_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF99-17_S20_L001_R2_001.fastq.unpaired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale python mapDamage -i ~/lus/museumDNA/RCF98-43_S11_L001_R12_001.fastq.paired.trim.sam.bam.rgi.bam.srt.bam.bam.mrkdup.bam -r ~/lus/new_genome_joint_call/alala-unzipArrow.fasta --rescale ############################# # SNP call (was run before and after rescaling of museum reads with MapDamage) #Take all the aligned reads and call SNPs from the data. The vcf format is "variant call format" and is human readable. ############################# /home/gblanche/apps/samtools/samtools-1.3.1/bin/samtools mpileup -uf alala-unzipArrow.fasta *.mrkdup*bam -q 20 -t AD,INFO/AD,DP | bcftools call -v -m -O v -f GQ > all_joint_newgenome.raw.vcf # Filter the SNPs using a Quality filter of 20 module load prod/bcftools-1.2 bcftools filter -i "Q>20" all_joint_newgenome.raw.vcf > all_joint_newgenome.q20.vcf # Calculate basic stats for your results:  for i in *.vcf; do bcftools stats $i > ${i/.vcf/_stats.txt}; done ############################ #Genotyping Individuals ############################ ############################ # Flagstat ############################ #Flagstat gives you the percent map per individual: # make an executable script with : module load bioinfo/samtools/1.1 #!/bin/bash for i in *.bam; do echo working with "$i" samtools flagstat $i > $i.flagstat done; # Get the # reads and % mapped by creating an executable script for every single flagstat file: cat file.flagstat | sed -n '5~13p' # Get the QC-passed by creating .sh for everysingle flagstat file: cat file | sed -n '1~13p'|awk '{print ($1)}' ############################# #Vcftools: ############################# #Depth ~/apps/vcftools_0.1.13/bin/vcftools --vcf GetVCFforRESCALEDq20.vcf --depth ~/apps/vcftools_0.1.13/bin/vcftools --vcf GetVCFforRESCALEDq20.vcf --remove-indels --depth ~/apps/vcftools_0.1.13/bin/vcftools --vcf GetVCFforRESCALEDq20.vcf --remove-indels --max-missing 0.5 --depth ~/apps/vcftools_0.1.13/bin/vcftools --vcf GetVCFforRESCALEDq20.vcf --remove-indels --max-missing 1 --depth ~/apps/vcftools_0.1.13/bin/vcftools --vcf GetVCFforRESCALEDq20.vcf --remove-indels --max-missing 0.5 --maf 0.1 --depth ~/apps/vcftools_0.1.13/bin/vcftools --vcf GetVCFforRESCALEDq20.vcf --min-meanDP 5 --remove-indels --max-missing 0.5 --maf 0.1 --depth #Remove individuals with min. mean Depth <5 after even after the above filters are applied: ~/apps/vcftools_0.1.13/bin/vcftools --vcf GetVCFforRESCALEDq20.vcf --remove-indv RCF99-17_S20 --remove-indv RCF98-09_S2 --remove-indv RCF98-53_S19 --remove-indv RCF98-52_S18 --remove-indv RCF98-48_S16 --remove-indv RCF98-44_S12 --remove-indv RCF98-16_S9 --remove-indv RCF98-15_S8 --remove-indv RCF98-15_S21 --remove-indv RCF98-14_S7 --remove-indv RCF98-13_S6 --remove-indv CH16_S24_L001 --remove-indv CH6_S14_L001 --remove-indv RCF98-08_S1 --remove-indels --min-meanDP 5 --max-missing 0.5 --maf 0.1 --depth ~/apps/vcftools_0.1.13/bin/vcftools --vcf GetVCFforRESCALEDq20.vcf --remove-indv RCF99-17_S20 --remove-indv RCF98-09_S2 --remove-indv RCF98-53_S19 --remove-indv RCF98-52_S18 --remove-indv RCF98-48_S16 --remove-indv RCF98-44_S12 --remove-indv RCF98-16_S9 --remove-indv RCF98-15_S8 --remove-indv RCF98-15_S21 --remove-indv RCF98-14_S7 --remove-indv RCF98-13_S6 --remove-indv CH16_S24_L001 --remove-indv CH6_S14_L001 --remove-indv RCF98-08_S1 --remove-indels --min-meanDP 5 --max-missing 1 --maf 0.1 --depth ~/apps/vcftools_0.1.13/bin/vcftools --vcf GetVCFforRESCALEDq20.vcf --remove-indv RCF99-17_S20 --remove-indv RCF98-09_S2 --remove-indv RCF98-53_S19 --remove-indv RCF98-52_S18 --remove-indv RCF98-48_S16 --remove-indv RCF98-44_S12 --remove-indv RCF98-16_S9 --remove-indv RCF98-15_S8 --remove-indv RCF98-15_S21 --remove-indv RCF98-14_S7 --remove-indv RCF98-13_S6 --remove-indv CH16_S24_L001 --remove-indv CH6_S14_L001 --remove-indv RCF98-08_S1 --remove-indels --min-meanDP 5 --max-missing 1 --maf 0.1 --relatedness ############################# #PED file creation: ############################# #Recode a new vcf file with filters and removed individuals: ~/apps/vcftools_0.1.13/bin/vcftools --vcf GetVCFforRESCALEDq20.vcf --remove-indv RCF99-17_S20 --remove-indv RCF98-09_S2 --remove-indv RCF98-53_S19 --remove-indv RCF98-52_S18 --remove-indv RCF98-48_S16 --remove-indv RCF98-44_S12 --remove-indv RCF98-16_S9 --remove-indv RCF98-15_S8 --remove-indv RCF98-15_S21 --remove-indv RCF98-14_S7 --remove-indv RCF98-13_S6 --remove-indv CH16_S24_L001 --remove-indv CH6_S14_L001 --remove-indv RCF98-08_S1 --remove-indels --min-meanDP 5 --max-missing 0.5 --maf 0.1 --recode --out NoMissingData ~/apps/vcftools_0.1.13/bin/vcftools --vcf GetVCFforRESCALEDq20.vcf --remove-indv RCF99-17_S20 --remove-indv RCF98-09_S2 --remove-indv RCF98-53_S19 --remove-indv RCF98-52_S18 --remove-indv RCF98-48_S16 --remove-indv RCF98-44_S12 --remove-indv RCF98-16_S9 --remove-indv RCF98-15_S8 --remove-indv RCF98-15_S21 --remove-indv RCF98-14_S7 --remove-indv RCF98-13_S6 --remove-indv CH16_S24_L001 --remove-indv CH6_S14_L001 --remove-indv RCF98-08_S1 --remove-indels --min-meanDP 5 --max-missing 1 --maf 0.1 --recode --out NoMissingData mv NoMissingData.recode.vcf NoMissingData.vcf #Make PED ~/apps/vcftools_0.1.13/bin/vcftools --vcf NoMissingData.vcf --plink --out NoMissingData After filtering, kept 310 out of a possible 310 Sites #Turn the PED file into txt cat NoMissingData.ped| sed 's/\t/\t/g'>NoMissingData.txt # Load R module load lang/R/3.3.2 #Make #pair_geno.nomissingdata.script.sh in HPC file #Import data data.frame<-read.table("NoMissingData.txt", header=FALSE,colClasses = c("character")) #pair the genotypes #made the pattern of paired numbers in Excel and then removed tab in Wrangler: NoMissingData <- data.frame(ID=(df[,1]),locus1=paste(df[,7],df[,8],sep=""),locus2=paste(df[,9],df[,10],sep=""),locus3=paste(df[,11],df[,12],sep=""),locus4=paste(df[,13],df[,14],sep=""),locus5=paste(df[,15],df[,16],sep=""),locus6=paste(df[,17],df[,18],sep=""),locus7=paste(df[,19],df[,20],sep=""),locus8=paste(df[,21],df[,22],sep=""),locus9=paste(df[,23],df[,24],sep=""),locus10=paste(df[,25],df[,26],sep=""),locus11=paste(df[,27],df[,28],sep=""),locus12=paste(df[,29],df[,30],sep=""),locus13=paste(df[,31],df[,32],sep=""),locus14=paste(df[,33],df[,34],sep=""),locus15=paste(df[,35],df[,36],sep=""),locus16=paste(df[,37],df[,38],sep=""),locus17=paste(df[,39],df[,40],sep=""),locus18=paste(df[,41],df[,42],sep=""),locus19=paste(df[,43],df[,44],sep=""),locus20=paste(df[,45],df[,46],sep=""),locus21=paste(df[,47],df[,48],sep=""),locus22=paste(df[,49],df[,50],sep=""),locus23=paste(df[,51],df[,52],sep=""),locus24=paste(df[,53],df[,54],sep=""),locus25=paste(df[,55],df[,56],sep=""),locus26=paste(df[,57],df[,58],sep=""),locus27=paste(df[,59],df[,60],sep=""),locus28=paste(df[,61],df[,62],sep=""),locus29=paste(df[,63],df[,64],sep=""),locus30=paste(df[,65],df[,66],sep=""),locus31=paste(df[,67],df[,68],sep=""),locus32=paste(df[,69],df[,70],sep=""),locus33=paste(df[,71],df[,72],sep=""),locus34=paste(df[,73],df[,74],sep=""),locus35=paste(df[,75],df[,76],sep=""),locus36=paste(df[,77],df[,78],sep=""),locus37=paste(df[,79],df[,80],sep=""),locus38=paste(df[,81],df[,82],sep=""),locus39=paste(df[,83],df[,84],sep=""),locus40=paste(df[,85],df[,86],sep=""),locus41=paste(df[,87],df[,88],sep=""),locus42=paste(df[,89],df[,90],sep=""),locus43=paste(df[,91],df[,92],sep=""),locus44=paste(df[,93],df[,94],sep=""),locus45=paste(df[,95],df[,96],sep=""),locus46=paste(df[,97],df[,98],sep=""),locus47=paste(df[,99],df[,100],sep=""),locus48=paste(df[,101],df[,102],sep=""),locus49=paste(df[,103],df[,104],sep=""),locus50=paste(df[,105],df[,106],sep=""),locus51=paste(df[,107],df[,108],sep=""),locus52=paste(df[,109],df[,110],sep=""),locus53=paste(df[,111],df[,112],sep=""),locus54=paste(df[,113],df[,114],sep=""),locus55=paste(df[,115],df[,116],sep=""),locus56=paste(df[,117],df[,118],sep=""),locus57=paste(df[,119],df[,120],sep=""),locus58=paste(df[,121],df[,122],sep=""),locus59=paste(df[,123],df[,124],sep=""),locus60=paste(df[,125],df[,126],sep=""),locus61=paste(df[,127],df[,128],sep=""),locus62=paste(df[,129],df[,130],sep=""),locus63=paste(df[,131],df[,132],sep=""),locus64=paste(df[,133],df[,134],sep=""),locus65=paste(df[,135],df[,136],sep=""),locus66=paste(df[,137],df[,138],sep=""),locus67=paste(df[,139],df[,140],sep=""),locus68=paste(df[,141],df[,142],sep=""),locus69=paste(df[,143],df[,144],sep=""),locus70=paste(df[,145],df[,146],sep=""),locus71=paste(df[,147],df[,148],sep=""),locus72=paste(df[,149],df[,150],sep=""),locus73=paste(df[,151],df[,152],sep=""),locus74=paste(df[,153],df[,154],sep=""),locus75=paste(df[,155],df[,156],sep=""),locus76=paste(df[,157],df[,158],sep=""),locus77=paste(df[,159],df[,160],sep=""),locus78=paste(df[,161],df[,162],sep=""),locus79=paste(df[,163],df[,164],sep=""),locus80=paste(df[,165],df[,166],sep=""),locus81=paste(df[,167],df[,168],sep=""),locus82=paste(df[,169],df[,170],sep=""),locus83=paste(df[,171],df[,172],sep=""),locus84=paste(df[,173],df[,174],sep=""),locus85=paste(df[,175],df[,176],sep=""),locus86=paste(df[,177],df[,178],sep=""),locus87=paste(df[,179],df[,180],sep=""),locus88=paste(df[,181],df[,182],sep=""),locus89=paste(df[,183],df[,184],sep=""),locus90=paste(df[,185],df[,186],sep=""),locus91=paste(df[,187],df[,188],sep=""),locus92=paste(df[,189],df[,190],sep=""),locus93=paste(df[,191],df[,192],sep=""),locus94=paste(df[,193],df[,194],sep=""),locus95=paste(df[,195],df[,196],sep=""),locus96=paste(df[,197],df[,198],sep=""),locus97=paste(df[,199],df[,200],sep=""),locus98=paste(df[,201],df[,202],sep=""),locus99=paste(df[,203],df[,204],sep=""),locus100=paste(df[,205],df[,206],sep=""),locus101=paste(df[,207],df[,208],sep=""),locus102=paste(df[,209],df[,210],sep=""),locus103=paste(df[,211],df[,212],sep=""),locus104=paste(df[,213],df[,214],sep=""),locus105=paste(df[,215],df[,216],sep=""),locus106=paste(df[,217],df[,218],sep=""),locus107=paste(df[,219],df[,220],sep=""),locus108=paste(df[,221],df[,222],sep=""),locus109=paste(df[,223],df[,224],sep=""),locus110=paste(df[,225],df[,226],sep=""),locus111=paste(df[,227],df[,228],sep=""),locus112=paste(df[,229],df[,230],sep=""),locus113=paste(df[,231],df[,232],sep=""),locus114=paste(df[,233],df[,234],sep=""),locus115=paste(df[,235],df[,236],sep=""),locus116=paste(df[,237],df[,238],sep=""),locus117=paste(df[,239],df[,240],sep=""),locus118=paste(df[,241],df[,242],sep=""),locus119=paste(df[,243],df[,244],sep=""),locus120=paste(df[,245],df[,246],sep=""),locus121=paste(df[,247],df[,248],sep=""),locus122=paste(df[,249],df[,250],sep=""),locus123=paste(df[,251],df[,252],sep=""),locus124=paste(df[,253],df[,254],sep=""),locus125=paste(df[,255],df[,256],sep=""),locus126=paste(df[,257],df[,258],sep=""),locus127=paste(df[,259],df[,260],sep=""),locus128=paste(df[,261],df[,262],sep=""),locus129=paste(df[,263],df[,264],sep=""),locus130=paste(df[,265],df[,266],sep=""),locus131=paste(df[,267],df[,268],sep=""),locus132=paste(df[,269],df[,270],sep=""),locus133=paste(df[,271],df[,272],sep=""),locus134=paste(df[,273],df[,274],sep=""),locus135=paste(df[,275],df[,276],sep=""),locus136=paste(df[,277],df[,278],sep=""),locus137=paste(df[,279],df[,280],sep=""),locus138=paste(df[,281],df[,282],sep=""),locus139=paste(df[,283],df[,284],sep=""),locus140=paste(df[,285],df[,286],sep=""),locus141=paste(df[,287],df[,288],sep=""),locus142=paste(df[,289],df[,290],sep=""),locus143=paste(df[,291],df[,292],sep=""),locus144=paste(df[,293],df[,294],sep=""),locus145=paste(df[,295],df[,296],sep=""),locus146=paste(df[,297],df[,298],sep=""),locus147=paste(df[,299],df[,300],sep=""),locus148=paste(df[,301],df[,302],sep=""),locus149=paste(df[,303],df[,304],sep=""),locus150=paste(df[,305],df[,306],sep=""),locus151=paste(df[,307],df[,308],sep=""),locus152=paste(df[,309],df[,310],sep=""),locus153=paste(df[,311],df[,312],sep=""),locus154=paste(df[,313],df[,314],sep=""),locus155=paste(df[,315],df[,316],sep=""),locus156=paste(df[,317],df[,318],sep=""),locus157=paste(df[,319],df[,320],sep=""),locus158=paste(df[,321],df[,322],sep=""),locus159=paste(df[,323],df[,324],sep=""),locus160=paste(df[,325],df[,326],sep=""),locus161=paste(df[,327],df[,328],sep=""),locus162=paste(df[,329],df[,330],sep=""),locus163=paste(df[,331],df[,332],sep=""),locus164=paste(df[,333],df[,334],sep=""),locus165=paste(df[,335],df[,336],sep=""),locus166=paste(df[,337],df[,338],sep=""),locus167=paste(df[,339],df[,340],sep=""),locus168=paste(df[,341],df[,342],sep=""),locus169=paste(df[,343],df[,344],sep=""),locus170=paste(df[,345],df[,346],sep=""),locus171=paste(df[,347],df[,348],sep=""),locus172=paste(df[,349],df[,350],sep=""),locus173=paste(df[,351],df[,352],sep=""),locus174=paste(df[,353],df[,354],sep=""),locus175=paste(df[,355],df[,356],sep=""),locus176=paste(df[,357],df[,358],sep=""),locus177=paste(df[,359],df[,360],sep=""),locus178=paste(df[,361],df[,362],sep=""),locus179=paste(df[,363],df[,364],sep=""),locus180=paste(df[,365],df[,366],sep=""),locus181=paste(df[,367],df[,368],sep=""),locus182=paste(df[,369],df[,370],sep=""),locus183=paste(df[,371],df[,372],sep=""),locus184=paste(df[,373],df[,374],sep=""),locus185=paste(df[,375],df[,376],sep=""),locus186=paste(df[,377],df[,378],sep=""),locus187=paste(df[,379],df[,380],sep=""),locus188=paste(df[,381],df[,382],sep=""),locus189=paste(df[,383],df[,384],sep=""),locus190=paste(df[,385],df[,386],sep=""),locus191=paste(df[,387],df[,388],sep=""),locus192=paste(df[,389],df[,390],sep=""),locus193=paste(df[,391],df[,392],sep=""),locus194=paste(df[,393],df[,394],sep=""),locus195=paste(df[,395],df[,396],sep=""),locus196=paste(df[,397],df[,398],sep=""),locus197=paste(df[,399],df[,400],sep=""),locus198=paste(df[,401],df[,402],sep=""),locus199=paste(df[,403],df[,404],sep=""),locus200=paste(df[,405],df[,406],sep=""),locus201=paste(df[,407],df[,408],sep=""),locus202=paste(df[,409],df[,410],sep=""),locus203=paste(df[,411],df[,412],sep=""),locus204=paste(df[,413],df[,414],sep=""),locus205=paste(df[,415],df[,416],sep=""),locus206=paste(df[,417],df[,418],sep=""),locus207=paste(df[,419],df[,420],sep=""),locus208=paste(df[,421],df[,422],sep=""),locus209=paste(df[,423],df[,424],sep=""),locus210=paste(df[,425],df[,426],sep=""),locus211=paste(df[,427],df[,428],sep=""),locus212=paste(df[,429],df[,430],sep=""),locus213=paste(df[,431],df[,432],sep=""),locus214=paste(df[,433],df[,434],sep=""),locus215=paste(df[,435],df[,436],sep=""),locus216=paste(df[,437],df[,438],sep=""),locus217=paste(df[,439],df[,440],sep=""),locus218=paste(df[,441],df[,442],sep=""),locus219=paste(df[,443],df[,444],sep=""),locus220=paste(df[,445],df[,446],sep=""),locus221=paste(df[,447],df[,448],sep=""),locus222=paste(df[,449],df[,450],sep=""),locus223=paste(df[,451],df[,452],sep=""),locus224=paste(df[,453],df[,454],sep=""),locus225=paste(df[,455],df[,456],sep=""),locus226=paste(df[,457],df[,458],sep=""),locus227=paste(df[,459],df[,460],sep=""),locus228=paste(df[,461],df[,462],sep=""),locus229=paste(df[,463],df[,464],sep=""),locus230=paste(df[,465],df[,466],sep=""),locus231=paste(df[,467],df[,468],sep=""),locus232=paste(df[,469],df[,470],sep=""),locus233=paste(df[,471],df[,472],sep=""),locus234=paste(df[,473],df[,474],sep=""),locus235=paste(df[,475],df[,476],sep=""),locus236=paste(df[,477],df[,478],sep=""),locus237=paste(df[,479],df[,480],sep=""),locus238=paste(df[,481],df[,482],sep=""),locus239=paste(df[,483],df[,484],sep=""),locus240=paste(df[,485],df[,486],sep=""),locus241=paste(df[,487],df[,488],sep=""),locus242=paste(df[,489],df[,490],sep=""),locus243=paste(df[,491],df[,492],sep=""),locus244=paste(df[,493],df[,494],sep=""),locus245=paste(df[,495],df[,496],sep=""),locus246=paste(df[,497],df[,498],sep=""),locus247=paste(df[,499],df[,500],sep=""),locus248=paste(df[,501],df[,502],sep=""),locus249=paste(df[,503],df[,504],sep=""),locus250=paste(df[,505],df[,506],sep=""),locus251=paste(df[,507],df[,508],sep=""),locus252=paste(df[,509],df[,510],sep=""),locus253=paste(df[,511],df[,512],sep=""),locus254=paste(df[,513],df[,514],sep=""),locus255=paste(df[,515],df[,516],sep=""),locus256=paste(df[,517],df[,518],sep=""),locus257=paste(df[,519],df[,520],sep=""),locus258=paste(df[,521],df[,522],sep=""),locus259=paste(df[,523],df[,524],sep=""),locus260=paste(df[,525],df[,526],sep=""),locus261=paste(df[,527],df[,528],sep=""),locus262=paste(df[,529],df[,530],sep=""),locus263=paste(df[,531],df[,532],sep=""),locus264=paste(df[,533],df[,534],sep=""),locus265=paste(df[,535],df[,536],sep=""),locus266=paste(df[,537],df[,538],sep=""),locus267=paste(df[,539],df[,540],sep=""),locus268=paste(df[,541],df[,542],sep=""),locus269=paste(df[,543],df[,544],sep=""),locus270=paste(df[,545],df[,546],sep=""),locus271=paste(df[,547],df[,548],sep=""),locus272=paste(df[,549],df[,550],sep=""),locus273=paste(df[,551],df[,552],sep=""),locus274=paste(df[,553],df[,554],sep=""),locus275=paste(df[,555],df[,556],sep=""),locus276=paste(df[,557],df[,558],sep=""),locus277=paste(df[,559],df[,560],sep=""),locus278=paste(df[,561],df[,562],sep=""),locus279=paste(df[,563],df[,564],sep=""),locus280=paste(df[,565],df[,566],sep=""),locus281=paste(df[,567],df[,568],sep=""),locus282=paste(df[,569],df[,570],sep=""),locus283=paste(df[,571],df[,572],sep=""),locus284=paste(df[,573],df[,574],sep=""),locus285=paste(df[,575],df[,576],sep=""),locus286=paste(df[,577],df[,578],sep=""),locus287=paste(df[,579],df[,580],sep=""),locus288=paste(df[,581],df[,582],sep=""),locus289=paste(df[,583],df[,584],sep=""),locus290=paste(df[,585],df[,586],sep=""),locus291=paste(df[,587],df[,588],sep=""),locus292=paste(df[,589],df[,590],sep=""),locus293=paste(df[,591],df[,592],sep=""),locus294=paste(df[,593],df[,594],sep=""),locus295=paste(df[,595],df[,596],sep=""),locus296=paste(df[,597],df[,598],sep=""),locus297=paste(df[,599],df[,600],sep=""),locus298=paste(df[,601],df[,602],sep=""),locus299=paste(df[,603],df[,604],sep=""),locus300=paste(df[,605],df[,606],sep=""),locus301=paste(df[,607],df[,608],sep=""),locus302=paste(df[,609],df[,610],sep=""),locus303=paste(df[,611],df[,612],sep=""),locus304=paste(df[,613],df[,614],sep=""),locus305=paste(df[,615],df[,616],sep=""),locus306=paste(df[,617],df[,618],sep=""),locus307=paste(df[,619],df[,620],sep=""),locus308=paste(df[,621],df[,622],sep="")) #then save the new 'genotype' dataframe write.table(NoMissingData,"NoMissingData.txt",sep="\t",row.names=FALSE) #this will save it as txt file in lus #Use txt file in R 3.3.3 for allele number, frequencing and heterozygosity comparison. ############################# # Relatedness: ############################# #used R instead #Before removing individuals: ~/apps/vcftools_0.1.13/bin/vcftools --vcf all_recalled.q20.vcf --remove-indels --min-meanDP 5 --max-missing 0.5 --maf 0.1 --relatedness #Remove individuals with min. mean depth <5 with all filters (--remove-indels --max-missing 0.5 --maf 0.1 --min-meanDP 5): ~/apps/vcftools_0.1.13/bin/vcftools --vcf all_recalled.q20.vcf --remove-indv RCF99-17_S20 --remove-indv RCF98-09_S2 --remove-indv RCF98-53_S19 --remove-indv RCF98-52_S18 --remove-indv RCF98-48_S16 --remove-indv RCF98-44_S12 --remove-indv RCF98-16_S9 --remove-indv RCF98-15_S8 --remove-indv RCF98-15_S21 --remove-indv RCF98-14_S7 --remove-indv RCF98-13_S6 --remove-indv CH16_S24_L001 --remove-indv CH6_S14_L001 --remove-indv RCF98-08_S1 --remove-indels --min-meanDP 5 --max-missing 0.5 --maf 0.1 --relatedness ############################# #Homozygosity and Inbreeding coefficient (F): ############################# #Used R instead ~/apps/vcftools_0.1.13/bin/vcftools --vcf rescale_filteredvcf.recode.vcf --het ############################# # Population Comparisons ############################# ############################# # PCA analysis with SNPRelate 1.8.0 in R 3.3.3 : ############################# #SNPrelate_Rscript #Import vcf file vcf.fn <- "/Users/genevieveblanchet/Desktop/PCA/rescale_filteredvcf.recode.vcf" #Transform vcf into gds file snpgdsVCF2GDS(vcf.fn, "resc_mrkdup_MODid.gds", method="biallelic.only") ## We used "biallelic.only" because method = "biallelic.only": to exact bi-allelic and polymorhpic SNP data (excluding monomorphic variants); method = "copy.num.of.ref": to extract and store dosage (0, 1, 2) of the reference allele for all variant sites, including bi-allelic SNPs, multi-allelic SNPs, indels and structural variants ############# # Next is used instead if we want monomorphic sites# #snpgdsVCF2GDS(vcf.fn, "test.gds", method="copy.num.of.ref") #summary of gds file snpgdsSummary("resc_mrkdup_MODid.gds") #Open the gds file as "genofile" genofile <- snpgdsOpen("resc_mrkdup_MODid.gds") #Do PCA with the "genofile" (I don't know what nb thread is) pca <- snpgdsPCA(genofile, num.thread=2) # variance proportion (%) pc.percent <- pca$varprop*100 head(round(pc.percent, 2)) #If there are population information, # Get sample id #sample.id <- read.gdsn(index.gdsn(genofile, "sample.id")) sample_id <- scan("/Users/genevieveblanchet/Desktop/PCA/sampleid.txt", what=character()) # Get population information #if it is stored in a text file "pop.txt" => I made a txt file with pop ID in same order than the sample ID pop_code <- scan("/Users/genevieveblanchet/Desktop/PCA/pop.txt", what=character()) # assume the order of sample IDs is as the same as population codes (this steps adds the pop ID to the sample IDs in the table) head(cbind(sample_id, pop_code)) tail(cbind(sample_id, pop_code)) # Make a data.frame tab <- data.frame(sample.id = factor(sample_id), pop = factor(pop_code), EV1 = pca$eigenvect[,1], # the first eigenvector EV2 = pca$eigenvect[,2], # the second eigenvector stringsAsFactors = FALSE) head(tab) tab # Draw plot(tab$EV2, tab$EV1, col=as.integer(tab$pop), xlim = c(-0.5, 0.5),xlab="eigenvector 2", ylim = c(-0.3, 0.3),ylab="eigenvector 1", main="PCA for 3,039 SNPs between\n Museum (MUS) and Modern (MOD)\n 'alalā samples") legend("bottomright", legend=levels(tab$pop), pch="o", col=1:nlevels(tab$pop)) #Add sample ID labels to points text(tab$EV2,tab$EV1, labels = tab[1:33,1], pos =2,cex=0.4 )