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Copy path11. Add read groups to BAM files, this done to keep the sample ids organized when creating the merged vcf file
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11. Add read groups to BAM files, this done to keep the sample ids organized when creating the merged vcf file
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#!/bin/bash
#SBATCH -n 8
#SBATCH --job-name=Bamtools_addReadGroups
#SBATCH -t 0-10:0
#SBATCH -A mwilsons
#SBATCH -o slurm.Bamtools_addReadGroups.out
#SBATCH -e slurm.Bamtools_addReadGroups.err
#SBATCH --mail-type=END,FAIL
#SBATCH [email protected]
#--------------------------
#--------------------------
# 1. start timer
#--------------------------
date
#--------------------------
# 2. move to directory and load programs
#--------------------------
cd scratch/kcolney/cancerCellLines_Haynes/2_data/BAM
module load java/latest
#--------------------------
# 3. BAMtools add read groups and index
#--------------------------
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH1_S1_L001.sort.markdup.bam OUTPUT=KH1_S1_L001.sort.markdup.readgrps.bam RGID=KH1_S1_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=BT474_C RGPL=ILLUMINA RGLB=KH1_S1_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH1_S1_L002.sort.markdup.bam OUTPUT=KH1_S1_L002.sort.markdup.readgrps.bam RGID=KH1_S1_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=BT474_C RGPL=ILLUMINA RGLB=KH1_S1_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH1_S1_L003.sort.markdup.bam OUTPUT=KH1_S1_L003.sort.markdup.readgrps.bam RGID=KH1_S1_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=BT474_C RGPL=ILLUMINA RGLB=KH1_S1_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH1_S1_L004.sort.markdup.bam OUTPUT=KH1_S1_L004.sort.markdup.readgrps.bam RGID=KH1_S1_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=BT474_C RGPL=ILLUMINA RGLB=KH1_S1_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH2_S2_L001.sort.markdup.bam OUTPUT=KH2_S2_L001.sort.markdup.readgrps.bam RGID=KH2_S2_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=BT474_C RGPL=ILLUMINA RGLB=KH2_S2_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH2_S2_L002.sort.markdup.bam OUTPUT=KH2_S2_L002.sort.markdup.readgrps.bam RGID=KH2_S2_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=BT474_C RGPL=ILLUMINA RGLB=KH2_S2_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH2_S2_L003.sort.markdup.bam OUTPUT=KH2_S2_L003.sort.markdup.readgrps.bam RGID=KH2_S2_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=BT474_C RGPL=ILLUMINA RGLB=KH2_S2_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH2_S2_L004.sort.markdup.bam OUTPUT=KH2_S2_L004.sort.markdup.readgrps.bam RGID=KH2_S2_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=BT474_C RGPL=ILLUMINA RGLB=KH2_S2_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH3_S3_L001.sort.markdup.bam OUTPUT=KH3_S3_L001.sort.markdup.readgrps.bam RGID=KH3_S3_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=BT474_24 RGPL=ILLUMINA RGLB=KH3_S3_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH3_S3_L002.sort.markdup.bam OUTPUT=KH3_S3_L002.sort.markdup.readgrps.bam RGID=KH3_S3_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=BT474_24 RGPL=ILLUMINA RGLB=KH3_S3_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH3_S3_L003.sort.markdup.bam OUTPUT=KH3_S3_L003.sort.markdup.readgrps.bam RGID=KH3_S3_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=BT474_24 RGPL=ILLUMINA RGLB=KH3_S3_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH3_S3_L004.sort.markdup.bam OUTPUT=KH3_S3_L004.sort.markdup.readgrps.bam RGID=KH3_S3_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=BT474_24 RGPL=ILLUMINA RGLB=KH3_S3_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH4_S4_L001.sort.markdup.bam OUTPUT=KH4_S4_L001.sort.markdup.readgrps.bam RGID=KH4_S4_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=BT474_24 RGPL=ILLUMINA RGLB=KH4_S4_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH4_S4_L002.sort.markdup.bam OUTPUT=KH4_S4_L002.sort.markdup.readgrps.bam RGID=KH4_S4_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=BT474_24 RGPL=ILLUMINA RGLB=KH4_S4_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH4_S4_L003.sort.markdup.bam OUTPUT=KH4_S4_L003.sort.markdup.readgrps.bam RGID=KH4_S4_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=BT474_24 RGPL=ILLUMINA RGLB=KH4_S4_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH4_S4_L004.sort.markdup.bam OUTPUT=KH4_S4_L004.sort.markdup.readgrps.bam RGID=KH4_S4_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=BT474_24 RGPL=ILLUMINA RGLB=KH4_S4_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH5_S5_L001.sort.markdup.bam OUTPUT=KH5_S5_L001.sort.markdup.readgrps.bam RGID=KH5_S5_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=BT474_48 RGPL=ILLUMINA RGLB=KH5_S5_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH5_S5_L002.sort.markdup.bam OUTPUT=KH5_S5_L002.sort.markdup.readgrps.bam RGID=KH5_S5_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=BT474_48 RGPL=ILLUMINA RGLB=KH5_S5_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH5_S5_L003.sort.markdup.bam OUTPUT=KH5_S5_L003.sort.markdup.readgrps.bam RGID=KH5_S5_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=BT474_48 RGPL=ILLUMINA RGLB=KH5_S5_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH5_S5_L004.sort.markdup.bam OUTPUT=KH5_S5_L004.sort.markdup.readgrps.bam RGID=KH5_S5_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=BT474_48 RGPL=ILLUMINA RGLB=KH5_S5_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH6_S6_L001.sort.markdup.bam OUTPUT=KH6_S6_L001.sort.markdup.readgrps.bam RGID=KH6_S6_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=BT474_48 RGPL=ILLUMINA RGLB=KH6_S6_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH6_S6_L002.sort.markdup.bam OUTPUT=KH6_S6_L002.sort.markdup.readgrps.bam RGID=KH6_S6_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=BT474_48 RGPL=ILLUMINA RGLB=KH6_S6_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH6_S6_L003.sort.markdup.bam OUTPUT=KH6_S6_L003.sort.markdup.readgrps.bam RGID=KH6_S6_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=BT474_48 RGPL=ILLUMINA RGLB=KH6_S6_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH6_S6_L004.sort.markdup.bam OUTPUT=KH6_S6_L004.sort.markdup.readgrps.bam RGID=KH6_S6_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=BT474_48 RGPL=ILLUMINA RGLB=KH6_S6_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH7_S7_L001.sort.markdup.bam OUTPUT=KH7_S7_L001.sort.markdup.readgrps.bam RGID=KH7_S7_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=BT474_72 RGPL=ILLUMINA RGLB=KH7_S7_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH7_S7_L002.sort.markdup.bam OUTPUT=KH7_S7_L002.sort.markdup.readgrps.bam RGID=KH7_S7_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=BT474_72 RGPL=ILLUMINA RGLB=KH7_S7_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH7_S7_L003.sort.markdup.bam OUTPUT=KH7_S7_L003.sort.markdup.readgrps.bam RGID=KH7_S7_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=BT474_72 RGPL=ILLUMINA RGLB=KH7_S7_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH7_S7_L004.sort.markdup.bam OUTPUT=KH7_S7_L004.sort.markdup.readgrps.bam RGID=KH7_S7_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=BT474_72 RGPL=ILLUMINA RGLB=KH7_S7_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH8_S8_L001.sort.markdup.bam OUTPUT=KH8_S8_L001.sort.markdup.readgrps.bam RGID=KH8_S8_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=BT474_72 RGPL=ILLUMINA RGLB=KH8_S8_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH8_S8_L002.sort.markdup.bam OUTPUT=KH8_S8_L002.sort.markdup.readgrps.bam RGID=KH8_S8_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=BT474_72 RGPL=ILLUMINA RGLB=KH8_S8_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH8_S8_L003.sort.markdup.bam OUTPUT=KH8_S8_L003.sort.markdup.readgrps.bam RGID=KH8_S8_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=BT474_72 RGPL=ILLUMINA RGLB=KH8_S8_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH8_S8_L004.sort.markdup.bam OUTPUT=KH8_S8_L004.sort.markdup.readgrps.bam RGID=KH8_S8_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=BT474_72 RGPL=ILLUMINA RGLB=KH8_S8_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH9_S1_L001.sort.markdup.bam OUTPUT=KH9_S1_L001.sort.markdup.readgrps.bam RGID=KH9_S1_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=BT549_C RGPL=ILLUMINA RGLB=KH9_S1_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH9_S1_L002.sort.markdup.bam OUTPUT=KH9_S1_L002.sort.markdup.readgrps.bam RGID=KH9_S1_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=BT549_C RGPL=ILLUMINA RGLB=KH9_S1_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH9_S1_L003.sort.markdup.bam OUTPUT=KH9_S1_L003.sort.markdup.readgrps.bam RGID=KH9_S1_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=BT549_C RGPL=ILLUMINA RGLB=KH9_S1_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH9_S1_L004.sort.markdup.bam OUTPUT=KH9_S1_L004.sort.markdup.readgrps.bam RGID=KH9_S1_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=BT549_C RGPL=ILLUMINA RGLB=KH9_S1_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH10_S2_L001.sort.markdup.bam OUTPUT=KH10_S2_L001.sort.markdup.readgrps.bam RGID=KH10_S2_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=BT549_C RGPL=ILLUMINA RGLB=KH10_S2_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH10_S2_L004.sort.markdup.bam OUTPUT=KH10_S2_L004.sort.markdup.readgrps.bam RGID=KH10_S2_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=BT549_C RGPL=ILLUMINA RGLB=KH10_S2_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH10_S2_L002.sort.markdup.bam OUTPUT=KH10_S2_L002.sort.markdup.readgrps.bam RGID=KH10_S2_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=BT549_C RGPL=ILLUMINA RGLB=KH10_S2_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH10_S2_L003.sort.markdup.bam OUTPUT=KH10_S2_L003.sort.markdup.readgrps.bam RGID=KH10_S2_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=BT549_C RGPL=ILLUMINA RGLB=KH10_S2_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH11_S3_L001.sort.markdup.bam OUTPUT=KH11_S3_L001.sort.markdup.readgrps.bam RGID=KH11_S3_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=BT549_24 RGPL=ILLUMINA RGLB=KH11_S3_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH11_S3_L002.sort.markdup.bam OUTPUT=KH11_S3_L002.sort.markdup.readgrps.bam RGID=KH11_S3_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=BT549_24 RGPL=ILLUMINA RGLB=KH11_S3_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH11_S3_L003.sort.markdup.bam OUTPUT=KH11_S3_L003.sort.markdup.readgrps.bam RGID=KH11_S3_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=BT549_24 RGPL=ILLUMINA RGLB=KH11_S3_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH11_S3_L004.sort.markdup.bam OUTPUT=KH11_S3_L004.sort.markdup.readgrps.bam RGID=KH11_S3_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=BT549_24 RGPL=ILLUMINA RGLB=KH11_S3_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH12_S4_L001.sort.markdup.bam OUTPUT=KH12_S4_L001.sort.markdup.readgrps.bam RGID=KH12_S4_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=BT549_24 RGPL=ILLUMINA RGLB=KH12_S4_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH12_S4_L002.sort.markdup.bam OUTPUT=KH12_S4_L002.sort.markdup.readgrps.bam RGID=KH12_S4_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=BT549_24 RGPL=ILLUMINA RGLB=KH12_S4_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH12_S4_L003.sort.markdup.bam OUTPUT=KH12_S4_L003.sort.markdup.readgrps.bam RGID=KH12_S4_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=BT549_24 RGPL=ILLUMINA RGLB=KH12_S4_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH12_S4_L004.sort.markdup.bam OUTPUT=KH12_S4_L004.sort.markdup.readgrps.bam RGID=KH12_S4_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=BT549_24 RGPL=ILLUMINA RGLB=KH12_S4_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH13_S5_L001.sort.markdup.bam OUTPUT=KH13_S5_L001.sort.markdup.readgrps.bam RGID=KH13_S5_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=BT549_48 RGPL=ILLUMINA RGLB=KH13_S5_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH13_S5_L002.sort.markdup.bam OUTPUT=KH13_S5_L002.sort.markdup.readgrps.bam RGID=KH13_S5_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=BT549_48 RGPL=ILLUMINA RGLB=KH13_S5_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH13_S5_L003.sort.markdup.bam OUTPUT=KH13_S5_L003.sort.markdup.readgrps.bam RGID=KH13_S5_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=BT549_48 RGPL=ILLUMINA RGLB=KH13_S5_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH13_S5_L004.sort.markdup.bam OUTPUT=KH13_S5_L004.sort.markdup.readgrps.bam RGID=KH13_S5_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=BT549_48 RGPL=ILLUMINA RGLB=KH13_S5_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH14_S6_L001.sort.markdup.bam OUTPUT=KH14_S6_L001.sort.markdup.readgrps.bam RGID=KH14_S6_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=BT549_48 RGPL=ILLUMINA RGLB=KH14_S6_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH14_S6_L002.sort.markdup.bam OUTPUT=KH14_S6_L002.sort.markdup.readgrps.bam RGID=KH14_S6_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=BT549_48 RGPL=ILLUMINA RGLB=KH14_S6_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH14_S6_L003.sort.markdup.bam OUTPUT=KH14_S6_L003.sort.markdup.readgrps.bam RGID=KH14_S6_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=BT549_48 RGPL=ILLUMINA RGLB=KH14_S6_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH14_S6_L004.sort.markdup.bam OUTPUT=KH14_S6_L004.sort.markdup.readgrps.bam RGID=KH14_S6_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=BT549_48 RGPL=ILLUMINA RGLB=KH14_S6_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH15_S7_L001.sort.markdup.bam OUTPUT=KH15_S7_L001.sort.markdup.readgrps.bam RGID=KH15_S7_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=BT549_72 RGPL=ILLUMINA RGLB=KH15_S7_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH15_S7_L002.sort.markdup.bam OUTPUT=KH15_S7_L002.sort.markdup.readgrps.bam RGID=KH15_S7_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=BT549_72 RGPL=ILLUMINA RGLB=KH15_S7_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH15_S7_L003.sort.markdup.bam OUTPUT=KH15_S7_L003.sort.markdup.readgrps.bam RGID=KH15_S7_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=BT549_72 RGPL=ILLUMINA RGLB=KH15_S7_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH15_S7_L004.sort.markdup.bam OUTPUT=KH15_S7_L004.sort.markdup.readgrps.bam RGID=KH15_S7_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=BT549_72 RGPL=ILLUMINA RGLB=KH15_S7_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH16_S8_L001.sort.markdup.bam OUTPUT=KH16_S8_L001.sort.markdup.readgrps.bam RGID=KH16_S8_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=BT549_72 RGPL=ILLUMINA RGLB=KH16_S8_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH16_S8_L002.sort.markdup.bam OUTPUT=KH16_S8_L002.sort.markdup.readgrps.bam RGID=KH16_S8_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=BT549_72 RGPL=ILLUMINA RGLB=KH16_S8_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH16_S8_L003.sort.markdup.bam OUTPUT=KH16_S8_L003.sort.markdup.readgrps.bam RGID=KH16_S8_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=BT549_72 RGPL=ILLUMINA RGLB=KH16_S8_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH16_S8_L004.sort.markdup.bam OUTPUT=KH16_S8_L004.sort.markdup.readgrps.bam RGID=KH16_S8_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=BT549_72 RGPL=ILLUMINA RGLB=KH16_S8_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH17_S9_L001.sort.markdup.bam OUTPUT=KH17_S9_L001.sort.markdup.readgrps.bam RGID=KH17_S9_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=MCF7_C RGPL=ILLUMINA RGLB=KH17_S9_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH17_S9_L002.sort.markdup.bam OUTPUT=KH17_S9_L002.sort.markdup.readgrps.bam RGID=KH17_S9_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=MCF7_C RGPL=ILLUMINA RGLB=KH17_S9_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH17_S9_L003.sort.markdup.bam OUTPUT=KH17_S9_L003.sort.markdup.readgrps.bam RGID=KH17_S9_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=MCF7_C RGPL=ILLUMINA RGLB=KH17_S9_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH17_S9_L004.sort.markdup.bam OUTPUT=KH17_S9_L004.sort.markdup.readgrps.bam RGID=KH17_S9_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=MCF7_C RGPL=ILLUMINA RGLB=KH17_S9_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH18_S9_L001.sort.markdup.bam OUTPUT=KH18_S9_L001.sort.markdup.readgrps.bam RGID=KH18_S9_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=MCF7_C RGPL=ILLUMINA RGLB=KH18_S9_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH18_S9_L002.sort.markdup.bam OUTPUT=KH18_S9_L002.sort.markdup.readgrps.bam RGID=KH18_S9_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=MCF7_C RGPL=ILLUMINA RGLB=KH18_S9_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH18_S9_L003.sort.markdup.bam OUTPUT=KH18_S9_L003.sort.markdup.readgrps.bam RGID=KH18_S9_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=MCF7_C RGPL=ILLUMINA RGLB=KH18_S9_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH18_S9_L004.sort.markdup.bam OUTPUT=KH18_S9_L004.sort.markdup.readgrps.bam RGID=KH18_S9_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=MCF7_C RGPL=ILLUMINA RGLB=KH18_S9_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH19_S10_L001.sort.markdup.bam OUTPUT=KH19_S10_L001.sort.markdup.readgrps.bam RGID=KH19_S10_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=MCF7_24 RGPL=ILLUMINA RGLB=KH19_S10_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH19_S10_L002.sort.markdup.bam OUTPUT=KH19_S10_L002.sort.markdup.readgrps.bam RGID=KH19_S10_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=MCF7_24 RGPL=ILLUMINA RGLB=KH19_S10_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH19_S10_L003.sort.markdup.bam OUTPUT=KH19_S10_L003.sort.markdup.readgrps.bam RGID=KH19_S10_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=MCF7_24 RGPL=ILLUMINA RGLB=KH19_S10_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH19_S10_L004.sort.markdup.bam OUTPUT=KH19_S10_L004.sort.markdup.readgrps.bam RGID=KH19_S10_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=MCF7_24 RGPL=ILLUMINA RGLB=KH19_S10_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH20_S10_L001.sort.markdup.bam OUTPUT=KH20_S10_L001.sort.markdup.readgrps.bam RGID=KH20_S10_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=MCF7_24 RGPL=ILLUMINA RGLB=KH20_S10_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH20_S10_L002.sort.markdup.bam OUTPUT=KH20_S10_L002.sort.markdup.readgrps.bam RGID=KH20_S10_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=MCF7_24 RGPL=ILLUMINA RGLB=KH20_S10_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH20_S10_L003.sort.markdup.bam OUTPUT=KH20_S10_L003.sort.markdup.readgrps.bam RGID=KH20_S10_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=MCF7_24 RGPL=ILLUMINA RGLB=KH20_S10_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH20_S10_L004.sort.markdup.bam OUTPUT=KH20_S10_L004.sort.markdup.readgrps.bam RGID=KH20_S10_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=MCF7_24 RGPL=ILLUMINA RGLB=KH20_S10_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH21_S11_L001.sort.markdup.bam OUTPUT=KH21_S11_L001.sort.markdup.readgrps.bam RGID=KH21_S11_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=MCF7_48 RGPL=ILLUMINA RGLB=KH21_S11_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH21_S11_L002.sort.markdup.bam OUTPUT=KH21_S11_L002.sort.markdup.readgrps.bam RGID=KH21_S11_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=MCF7_48 RGPL=ILLUMINA RGLB=KH21_S11_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH21_S11_L003.sort.markdup.bam OUTPUT=KH21_S11_L003.sort.markdup.readgrps.bam RGID=KH21_S11_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=MCF7_48 RGPL=ILLUMINA RGLB=KH21_S11_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH21_S11_L004.sort.markdup.bam OUTPUT=KH21_S11_L004.sort.markdup.readgrps.bam RGID=KH21_S11_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=MCF7_48 RGPL=ILLUMINA RGLB=KH21_S11_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH22_S11_L001.sort.markdup.bam OUTPUT=KH22_S11_L001.sort.markdup.readgrps.bam RGID=KH22_S11_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=MCF7_48 RGPL=ILLUMINA RGLB=KH22_S11_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH22_S11_L002.sort.markdup.bam OUTPUT=KH22_S11_L002.sort.markdup.readgrps.bam RGID=KH22_S11_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=MCF7_48 RGPL=ILLUMINA RGLB=KH22_S11_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH22_S11_L003.sort.markdup.bam OUTPUT=KH22_S11_L003.sort.markdup.readgrps.bam RGID=KH22_S11_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=MCF7_48 RGPL=ILLUMINA RGLB=KH22_S11_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH22_S11_L004.sort.markdup.bam OUTPUT=KH22_S11_L004.sort.markdup.readgrps.bam RGID=KH22_S11_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=MCF7_48 RGPL=ILLUMINA RGLB=KH22_S11_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH23_S12_L001.sort.markdup.bam OUTPUT=KH23_S12_L001.sort.markdup.readgrps.bam RGID=KH23_S12_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=MCF7_72 RGPL=ILLUMINA RGLB=KH23_S12_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH23_S12_L002.sort.markdup.bam OUTPUT=KH23_S12_L002.sort.markdup.readgrps.bam RGID=KH23_S12_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=MCF7_72 RGPL=ILLUMINA RGLB=KH23_S12_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH23_S12_L003.sort.markdup.bam OUTPUT=KH23_S12_L003.sort.markdup.readgrps.bam RGID=KH23_S12_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=MCF7_72 RGPL=ILLUMINA RGLB=KH23_S12_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH23_S12_L004.sort.markdup.bam OUTPUT=KH23_S12_L004.sort.markdup.readgrps.bam RGID=KH23_S12_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=MCF7_72 RGPL=ILLUMINA RGLB=KH23_S12_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH24_S12_L001.sort.markdup.bam OUTPUT=KH24_S12_L001.sort.markdup.readgrps.bam RGID=KH24_S12_L001 RGPU=NB501259_55_HFFGNBGXY.1 RGSM=MCF7_72 RGPL=ILLUMINA RGLB=KH24_S12_L001 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH24_S12_L002.sort.markdup.bam OUTPUT=KH24_S12_L002.sort.markdup.readgrps.bam RGID=KH24_S12_L002 RGPU=NB501259_55_HFFGNBGXY.2 RGSM=MCF7_72 RGPL=ILLUMINA RGLB=KH24_S12_L002 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH24_S12_L003.sort.markdup.bam OUTPUT=KH24_S12_L003.sort.markdup.readgrps.bam RGID=KH24_S12_L003 RGPU=NB501259_55_HFFGNBGXY.3 RGSM=MCF7_72 RGPL=ILLUMINA RGLB=KH24_S12_L003 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
java -Xmx8g -jar /home/kcolney/ngcchome/tools2/picard.jar AddOrReplaceReadGroups INPUT=KH24_S12_L004.sort.markdup.bam OUTPUT=KH24_S12_L004.sort.markdup.readgrps.bam RGID=KH24_S12_L004 RGPU=NB501259_55_HFFGNBGXY.4 RGSM=MCF7_72 RGPL=ILLUMINA RGLB=KH24_S12_L004 RGCN=ArizonaStateUniversity RGDS=homosapien VALIDATION_STRINGENCY=LENIENT
#--------------------------
# 4. end timer
#--------------------------
date