def runPicard(listOfBams):
readGroupsCommands = []
markDuplicatesCommands = []
for bamFile in listOfBams:
cellLine = fileUtil.getCellLineFromFilename(bamFile)
# Runs AddOrReplaceReadGroups
# Template: java -Xmx8g -jar ~/software/picard/picard/dist/picard.jar AddOrReplaceReadGroups I=star_output.sam O=rg_added_sorted.bam SO=coordinate RGID=id RGLB=library RGPL=platform RGPU=machine RGSM=sample
commandTemplate = "java -Xmx8g -jar ~/software/picard/picard/dist/picard.jar AddOrReplaceReadGroups I=%s O=%s_rg_added_sorted.bam SO=coordinate RGID=1 RGLB=illumina RGPL=illumina RGPU=illumina RGSM=%s"
command = commandTemplate % (bamFile, cellLine, cellLine)
readGroupsCommands.append(command)
# command = command + bamFile + " "
# command = command + "O=" + cellLine + "_rg_added_sorted.bam "
# command = command + "SO=coordinate RGID=1 RGLB=illumina RGPL=illumina RGPU=illumina RGSM=" + cellLine + "\n"
# outputScript.write(command)
# Runs MarkDuplicates
# Template: java -jar MarkDuplicates I=rg_added_sorted.bam O=dedupped.bam CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT M=output.metrics
commandTemplate = "java -Xmx8g -jar ~/software/picard/picard/dist/picard.jar MarkDuplicates I=%s_rg_added_sorted.bam O=%s_dedupped.bam CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT M=%s_dedupped.metrics"
command = commandTemplate % (cellLine, cellLine, cellLine)
markDuplicatesCommands.append(command)
# command = command + "O=" + cellLine + "_dedupped.bam "
# command = command + "CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT M=" + cellLine + "output.metrics\n"
# outputScript.write(command)
# outputScript.write("\n")
s.executeFunctions(readGroupsCommands, parallel = True, simulate = True)
s.executeFunctions(markDuplicatesCommands, parallel = True, simulate = True)
- NORMAL .bam file
- TUMOR .bam file
It automatically the outputfile name as well as the log filename based on
these .bam file inputs. The .bam files must have been processed already by
Picard and splitNCigarReads, which can be run by runPicard.py and
runSplitNCigarReads.py, respectively.
Written by Kevin Wu, Ortiz Lab UCSF, August 2015
"""
import subprocess
import sys
sys.path.append("/home/ortiz-lab/Documents/kwu/scripts/util/")
import fileUtil as f
import shellUtil as s
if len(sys.argv) != 3:
print("Error. Wrong number of arguments.")
print(helpDoc)
exit()
# (normalBam, tumorBam, outputFile, logFile)
normalBam = sys.argv[1]
tumorBam = sys.argv[2]
outputFile = "%s_normal_vs_%s_tumor_mutect.out" % (f.getCellLineFromFilename(normalBam), f.getCellLineFromFilename(tumorBam))
logFile = outputFile + ".log"
command = "java -Xmx8g -jar /home/ortiz-lab/software/muTect/mutect-1.1.7.jar --analysis_type MuTect --reference_sequence /media/Data/genomes/hg19_ordered/hg19.fa --cosmic /home/ortiz-lab/software/muTect/bundle/liftedover_output_hg19.vcf --dbsnp /home/ortiz-lab/software/muTect/bundle/dbsnp_138.hg19.excluding_sites_after_129.vcf --input_file:normal %s --input_file:tumor %s --out %s -log %s" % (normalBam, tumorBam, outputFile, logFile)
print(command)
subprocess.call(command, shell = True)