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06-mergeBAM_callSNPs_initial.py
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06-mergeBAM_callSNPs_initial.py
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#! /usr/bin/env python
# PBS cluster job submission in Python
# Use picard to merge realigned-around-indel BAM files then makes index
# Then call SNPs with GATK-3.3.0
# By Jean P. Elbers
# Last modified 22 Jan 2015
###############################################################################
Usage = """
06-mergeBAM_callSNPs_initial.py - version 1.0
Command:
cd InDir = /work/jelber2/immunome_2014/combined/realign-around-indels
1.Merge Bam files
java -Xmx8g -jar ~/bin/picard-tools-1.128/picard.jar MergeSamFiles \
SO=coordinate \
AS=true \
CREATE_INDEX=true \
I=Sample1-realigned.bam \
I=Sample2-realigned.bam \
O=../call-SNPs-initial/ALL-samples-initial.bam
2.Call SNPs
java -Xmx8g -jar ~/bin/GATK-3.3.0/GenomeAnalysisTK.jar \
-T UnifiedGenotyper \
-R RefDir/GCF_000241765.3_Chrysemys_picta_bellii-3.0.3_genomic.fna \
-I ../call-SNPs-initial/ALL-samples-initial.bam \
-L /work/jelber2/reference/immunome_baits_C_picta-3.0.3.interval.list \
-maxAltAlleles 32 \
-gt_mode DISCOVERY \
-stand_call_conf 30 \
-stand_emit_conf 10 \
-o ../call-SNPs-initial/ALL-samples-initial-Q30-rawSNPS.vcf
3.Call Indels
java -Xmx8g -jar ~/bin/GATK-3.3.0/GenomeAnalysisTK.jar \
-T UnifiedGenotyper \
-R RefDir/GCF_000241765.3_Chrysemys_picta_bellii-3.0.3_genomic.fna \
-I ../call-SNPs-initial/ALL-samples-initial.bam \
-L /work/jelber2/reference/immunome_baits_C_picta-3.0.3.interval.list \
-maxAltAlleles 32 \
-gt_mode DISCOVERY \
-glm INDEL \
-stand_call_conf 30 \
-stand_emit_conf 10 \
-o ../call-SNPs-initial/ALL-samples-initial-Q30-indels.vcf
4.Filter SNP calls around indels
java -Xmx8g -jar ~/bin/GATK-3.3.0/GenomeAnalysisTK.jar \
-T VariantFiltration \
-R RefDir/GCF_000241765.3_Chrysemys_picta_bellii-3.0.3_genomic.fna \
-L /work/jelber2/reference/immunome_baits_C_picta-3.0.3.interval.list \
-V ../call-SNPs-initial/ALL-samples-initial-Q30-rawSNPS.vcf \
--mask ../call-SNPs-initial/ALL-samples-initial-Q30-indels.vcf \
--maskExtension 5 \
--maskName InDel \
--clusterWindowSize 10 \
--filterExpression "MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1)" \
--filterName "Bad Validation" \
--filterExpression "QUAL < 30.0" \
--filterName "LowQual" \
--filterExpression "QD < 2.0" \
--filterName "Low Variant Confidence" \
--genotypeFilterExpression "DP < 10.0" \
--genotypeFilterName "Low Read Depth Over Sample" \
--genotypeFilterExpression "GQ < 20.0" \
--genotypeFilterName "Low GenotypeQuality" \
-o ../call-SNPs-initial/ALL-samples-initial-Q30-SNPs.vcf
File Info:
InDir = /work/jelber2/immunome_2014/combined/realign-around-indels
Input Files = *-realigned.bam
OutDir = /work/jelber2/immunome_2014/combined/call-SNPs-initial
Output Files = ALL-samples-initial.bam
ALL-samples-initial-Q30-SNPs.vcf
Usage (execute following code in InDir):
~/scripts/immunome_2014/06-mergeBAM_callSNPs_initial.py *-realigned.bam
"""
###############################################################################
import os, sys, subprocess #imports os, sys, subprocess modules
if len(sys.argv)<2:
print Usage
else:
FileList = sys.argv[1:]
IFileList =[]
for File in FileList:
IFile = "I="+File+" \\"
IFileList.append(IFile)
IFileListString = '\n'.join(IFileList)
FileList = sys.argv[1:]
RefDir = "/work/jelber2/reference"
InDir = "/work/jelber2/immunome_2014/combined/realign-around-indels"
OutDir1 = "call-SNPs-initial"
os.chdir(InDir)
os.chdir("..") # go up one directory
if not os.path.exists(OutDir1):
os.mkdir(OutDir1) # if OutDir1 does not exist, make it
os.chdir(InDir)
# Customize your options here
Queue = "single"
Allocation = "hpc_gopo02"
Processors = "nodes=1:ppn=4"
WallTime = "04:00:00"
LogOut = "/work/jelber2/immunome_2014/combined/call-SNPs-initial"
LogMerge = "oe"
JobName = "mergeBAM_callSNPs_initial"
Command ="""
java -Xmx8g -jar ~/bin/picard-tools-1.128/picard.jar MergeSamFiles \
SO=coordinate \
AS=true \
CREATE_INDEX=true \
%s
O=../call-SNPs-initial/ALL-samples-initial.bam
java -Xmx8g -jar ~/bin/GATK-3.3.0/GenomeAnalysisTK.jar \
-T UnifiedGenotyper \
-R %s/GCF_000241765.3_Chrysemys_picta_bellii-3.0.3_genomic.fna \
-I ../call-SNPs-initial/ALL-samples-initial.bam \
-L /work/jelber2/reference/immunome_baits_C_picta-3.0.3.interval.list \
-maxAltAlleles 32 \
-gt_mode DISCOVERY \
-stand_call_conf 30 \
-stand_emit_conf 10 \
-o ../call-SNPs-initial/ALL-samples-initial-Q30-rawSNPS.vcf
java -Xmx8g -jar ~/bin/GATK-3.3.0/GenomeAnalysisTK.jar \
-T UnifiedGenotyper \
-R %s/GCF_000241765.3_Chrysemys_picta_bellii-3.0.3_genomic.fna \
-I ../call-SNPs-initial/ALL-samples-initial.bam \
-L /work/jelber2/reference/immunome_baits_C_picta-3.0.3.interval.list \
-maxAltAlleles 32 \
-gt_mode DISCOVERY \
-glm INDEL \
-stand_call_conf 30 \
-stand_emit_conf 10 \
-o ../call-SNPs-initial/ALL-samples-initial-Q30-indels.vcf
java -Xmx8g -jar ~/bin/GATK-3.3.0/GenomeAnalysisTK.jar \
-T VariantFiltration \
-R %s/GCF_000241765.3_Chrysemys_picta_bellii-3.0.3_genomic.fna \
-L /work/jelber2/reference/immunome_baits_C_picta-3.0.3.interval.list \
-V ../call-SNPs-initial/ALL-samples-initial-Q30-rawSNPS.vcf \
--mask ../call-SNPs-initial/ALL-samples-initial-Q30-indels.vcf \
--maskExtension 5 \
--maskName InDel \
--clusterWindowSize 10 \
--filterExpression "MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1)" \
--filterName "Bad Validation" \
--filterExpression "QUAL < 30.0" \
--filterName "LowQual" \
--filterExpression "QD < 2.0" \
--filterName "Low Variant Confidence" \
--genotypeFilterExpression "DP < 10.0" \
--genotypeFilterName "Low Read Depth Over Sample" \
--genotypeFilterExpression "GQ < 20.0" \
--genotypeFilterName "Low GenotypeQuality" \
-o ../call-SNPs-initial/ALL-samples-initial-Q30-SNPs.vcf""" % \
(IFileListString,
RefDir,
RefDir,
RefDir)
JobString = """
#!/bin/bash
#PBS -q %s
#PBS -A %s
#PBS -l %s
#PBS -l walltime=%s
#PBS -o %s
#PBS -j %s
#PBS -N %s
cd %s
%s\n""" % (Queue, Allocation, Processors, WallTime, LogOut, LogMerge, JobName, InDir, Command)
#Create pipe to qsub
proc = subprocess.Popen(['qsub'], shell=True,
stdin=subprocess.PIPE, stdout=subprocess.PIPE, close_fds=True)
(child_stdout, child_stdin) = (proc.stdout, proc.stdin)
#Print JobString
JobName = proc.communicate(JobString)[0]
print JobString
print JobName