def SelectVariants(path, vcf, reference, sample_name, log, workdir):
start_time = datetime.datetime.now()
out_vcf = workdir + '/' + sample_name + '.GATK.vcf'
version = check_version_gatk(path, log)
if version.startswith('3'):
args = [
'java', '-Xmx' + ram, '-jar', path, '-T', 'SelectVariants', '-R',
reference, '-o', out_vcf
]
elif version.startswith('4.1'):
args = [
path, 'SelectVariants', '-R', reference, '-O', out_vcf,
'--keep-original-ac'
]
args += ['-V', vcf]
args += ['--sample-name', sample_name]
success = subprocess.call(args, stdout=log, stderr=log)
#success = 0
elapsed_time = divmod(
(datetime.datetime.now() - start_time).total_seconds(), 60)
if not success:
#print("- CombineGVCFs " +sample_name + ": %d min, %d sec" % elapsed_time)
return out_vcf
else:
f.prRed('Error in SelectVariants: ' + vcf + '. Check log file.')
exit(1)
def VariantAnnotator(path, vcf, reference, bam, target, log, workdir):
start_time = datetime.datetime.now()
out_vcf = workdir + '/' + '.'.join(
vcf.split('/')[-1].split('.')[:-1] + ['VA.vcf'])
version = check_version_gatk(path, log)
if version.startswith('3'):
args = [
'java', '-Xmx' + ram, '-jar', path, '-T', 'VariantAnnotator', '-R',
reference, '-o', out_vcf
]
elif version.startswith('4.1'):
args = [path, 'VariantAnnotator', '-R', reference, '-O', out_vcf]
args += ['-V', vcf, '-I', bam]
#args += ['-G','AS_StandardAnnotation']
#args += ['--enable-all-annotations']
#args += ['-G','StandardAnnotation']
#args += ['-A', 'TandemRepeat']
if target != None:
args += ['-L', target]
print(' '.join(args))
success = subprocess.call(args, stdout=log, stderr=log)
#success = 0
elapsed_time = divmod(
(datetime.datetime.now() - start_time).total_seconds(), 60)
if not success:
#print("- CombineGVCFs " +sample_name + ": %d min, %d sec" % elapsed_time)
return out_vcf
else:
f.prRed('Error in VariantAnnotator: ' + vcf + '. Check log file.')
exit(1)
def Vep(path, fork, name, reference, transcript_list, vep_af, vep_plugins, vcf,
log, workdir):
vep_vcf = workdir + '/' + name + '.VEP.vcf'
args = [
path, '-i', vcf, '-o', vep_vcf, '--species', 'homo_sapiens',
'--assembly', 'GRCh37', '--force_overwrite', '--no_stats', '--cache',
'--offline', '--fasta', reference, '--merged', '--sift', 'b',
'--polyphen', 'b', '--numbers', '--vcf_info_field', 'ANN', '--hgvs',
'--transcript_version', '--symbol', '--canonical', '--check_existing',
'--vcf', '--fork', fork, '--use_given_ref'
]
if vep_af != "":
for v in vep_af.split(','):
args += [v]
if vep_plugins['list'] != '':
args += add_vep_plugins(vep_plugins)
if transcript_list == None:
args += ['--pick']
if transcript_list == "most_severe":
args += ['--most_severe']
#print(' '.join(args))
success = subprocess.call(args, stdout=log, stderr=log)
if not success:
print("- VEP: " + name)
return vep_vcf
else:
f.prRed('Error in VEP annotation. Check log file.' + log)
exit(1)
def iEVA(path, vcf, reference, bam_list, log, workdir):
ieva_vcf = workdir + '/' + '.'.join(
vcf.split('/')[-1].split('.')[:-1] + ['iEVA.vcf'])
args = [
'python2', path, '--input', vcf, '--reference', reference, '--list',
bam_list, '--outfile', ieva_vcf
]
args += [
"--SimpleRepeat", "--SimpleRepeatLength",
"--PseudoNucleotidesComposition", "--RepeatMasker", "--gcContent",
"--VariantClass", "--StrandBiasReads", "--UnMappedReads",
"--MappingQualityZero", "--NotPrimaryAlignment",
"--SupplementaryAlignment", "--NotPairedReads",
"--NotProperPairedReads", "--AlignmentScore", "--NumberTotalDupReads",
"--NumberReadDupRef", "--NumberReadDupAlt", "--DuplicateReference",
"--DuplicateAlternate", "--DeltaDuplicate", "--iEvaDepth",
"--iAlleleDepth", "--ReadRef", "--ReadAlt", "--MeanRefQscore",
"--MeanAltQscore", "--TotalDPUnfilter", "--NumberClippedReadsRef",
"--NumberClippedReadsAlt", "--ClippedReadsRef", "--ClippedReadsAlt"
]
success = subprocess.call(args, stdout=log, stderr=log)
if not success:
return ieva_vcf
else:
f.prRed('Error in iEVA annotation. Check log file.')
exit(1)
def mpileup(name, reference, gbam, sbam, bam_list, target, log, workdir):
start_time = datetime.datetime.now()
#print("- Mpileup")
mpileup = workdir + '/' + name + '.mpileup'
open_mpileup = open(mpileup, 'w')
args = [
'samtools', 'mpileup', '-B', '-q 1', '-d', '50000', '-L', '50000',
'-f', reference
]
if sbam != None:
args += [sbam]
if gbam != None:
args += [gbam]
if bam_list != None:
args += ['-b', bam_list]
if target != None:
args += ['-l', target]
success = subprocess.call(args, stdout=open_mpileup, stderr=log)
#success= 0
elapsed_time = divmod(
(datetime.datetime.now() - start_time).total_seconds(), 60)
open_mpileup.close()
if not success:
print("- Mpileup: %d min, %d sec" % elapsed_time)
return mpileup
else:
f.prRed('Error in Mpileup. Check log file.')
exit(1)
def features_extractor(path, outpath, gatk, freebayes, varscan, merge,
features_list, gvcf_path, design, log, workdir):
start_time = datetime.datetime.now()
args = [
'python2', path, '--listaFeatures', features_list, '--gvcf_path',
gvcf_path, '-o', outpath
]
tsvfile = outpath + '/tsv.list'
if merge:
args += ['--merge', merge]
if gatk:
args += ['-g', gatk]
if freebayes:
args += ['-f', freebayes]
if varscan:
args += ['-v']
# if design == "Amplicon":
# args += ['-a']
success = subprocess.call(args, stderr=log)
elapsed_time = divmod(
(datetime.datetime.now() - start_time).total_seconds(), 60)
if not success:
#print("- Estraction: %d min, %d sec" % elapsed_time)
return merge, tsvfile
else:
f.prRed('Error in features extraction. Check log file.')
exit(1)
def CombineGVCFs(path, ram, gvcf_array, sample_name, reference, target, log,
workdir):
start_time = datetime.datetime.now()
gvcf_cohort = workdir + '/' + sample_name + '.g.vcf'
version = check_version_gatk(path, log)
if version.startswith('3'):
args = [
'java', '-Xmx' + ram, '-jar', path, '-T', 'CombineGVCFs', '-R',
reference, '-o', gvcf_cohort
]
elif version.startswith('4.1'):
args = [path, 'CombineGVCFs', '-R', reference, '-O', gvcf_cohort]
#args += ['-G','AS_StandardAnnotation']
args += ['--enable-all-annotations']
if target != None:
args += ['-L', target]
for gvcf in gvcf_array:
args += ['-V', gvcf]
success = subprocess.call(args, stdout=log, stderr=log)
#success = 0
elapsed_time = divmod(
(datetime.datetime.now() - start_time).total_seconds(), 60)
if not success:
#print("- CombineGVCFs " +sample_name + ": %d min, %d sec" % elapsed_time)
return gvcf_cohort
else:
f.prRed('Error in CombineGVCFs: ' + sample_name + '. Check log file.')
exit(1)
def GenotypeGVCFs(path, ram, gvcf, name, reference, target, log, workdir):
start_time = datetime.datetime.now()
version = check_version_gatk(path, log)
#print('version',version)
#print("- GenotypeGVCFs")
vcf = workdir + '/' + name + '.GATK.vcf'
if version.startswith('3'):
args = [
'java', '-Xmx' + ram, '-jar', path, '-T', 'GenotypeGVCFs', '-R',
reference, '-V:VCF', gvcf, '-o', vcf
]
elif version.startswith('4.1'):
args = [path, 'GenotypeGVCFs', '-R', reference, '-V', gvcf, '-O', vcf]
#args += ['-G','AS_StandardAnnotation']
args += ['--java-options', '-Xmx' + ram]
#args += ['--enable-all-annotations']
args += ['-A', 'StrandBiasBySample']
if target != None:
args += ['-L', target]
success = subprocess.call(args, stdout=log, stderr=log)
#success =0
elapsed_time = divmod(
(datetime.datetime.now() - start_time).total_seconds(), 60)
if not success:
print("- GenotypeGVCFs: %d min, %d sec" % elapsed_time)
return vcf
else:
f.prRed('Error in GenotypeGVCFs. Check log file.')
exit(1)
def BaseRecalibrator(path, ram, bam, reference, dbsnp, mills, target, log,
workdir):
#print("- Base quality score recalibration")
outbam = workdir + '/' + '.'.join(
bam.split('/')[-1].split('.')[:-1] + ['BQSR'] + ['bam'])
table = workdir + '/' + '.'.join(
bam.split('/')[-1].split('.')[:-1] + ['BQSR'] + ['table'])
args = [
'java', '-Xmx' + ram, '-jar', path, '-T', 'BaseRecalibrator', '-R',
reference, '-I', bam, '-o', table, '-knownSites', dbsnp, '-knownSites',
mills, '-L', target
]
#args = [path,'BaseRecalibrator','-R',reference,'-I', bam,'-o',table,'-knownSites',dbsnp,'-knownSites',mills,'-L',target]
success = subprocess.call(args, stdout=log, stderr=log)
if not success:
pass
else:
f.prRed(
'Error in table creation for Base quality score recalibration. Check log file.'
)
exit(1)
args = [
'java', '-Xmx' + ram, '-jar', path, '-T', 'PrintReads', '-R',
reference, '-I', bam, '-BQSR', table, '-L', target, '-o', outbam
]
success = subprocess.call(args, stdout=log, stderr=log)
if not success:
return outbam
else:
f.prRed('Error in base quality score recalibration. Check log file.')
exit(1)
def VarScan_somatic(path, ram, gpileup, spileup, reference, target, log,
workdir):
start_time = datetime.datetime.now()
#print("- VarScan mpileup2indel")
vcf = workdir + '/' + '.'.join(
spileup.split('/')[-1].split('.')[:-1] + ['VarScan'])
snp = vcf + '.snp.vcf'
indel = vcf + '.indel.vcf'
#args = ['java','-Xmx'+ram,'-jar',path,'somatic',gpileup,spileup,vcf,'--output-vcf','1','--strand-filter 0','--mpileup 1']
args = [
'java', '-Xmx' + ram, '-jar', path, 'somatic', spileup, vcf,
'--output-vcf', '1', '--strand-filter', '0', '--mpileup', '1'
]
if target != None:
args += ['-L', target]
#if filters == '0':
#args += ['--min-coverage','1','--min-var-freq','0.01','--min-reads2','1','--min-avg-qual','0','--p-value','0.95']
success = subprocess.call(args, stdout=log, stderr=log)
elapsed_time = divmod(
(datetime.datetime.now() - start_time).total_seconds(), 60)
if not success:
print("- VarScan mpileup2somatic: %d min, %d sec" % elapsed_time)
return snp, indel
#return vcf
else:
f.prRed('Error in VarScan mpileup2somatic. Check log file.')
exit(1)
def VarScan_mpileup2indel(path, ram, mpileup, sample_list, reference, target,
log, workdir):
start_time = datetime.datetime.now()
#print("- VarScan mpileup2indel")
vcf = workdir + '/' + '.'.join(
mpileup.split('/')[-1].split('.')[:-1] + ['VarScan.indel.vcf'])
open_vcf = open(vcf, 'w')
args = [
'java', '-Xmx' + ram, '-jar', path, 'mpileup2indel', mpileup,
'--vcf-sample-list', sample_list, '--output-vcf', '1',
'--strand-filter 0'
]
if target != None:
args += ['-L', target]
#if filters == '0':
args += [
'--min-coverage', '1', '--min-var-freq', '0.01', '--min-reads2', '1',
'--min-avg-qual', '0', '--p-value', '0.95'
]
success = subprocess.call(args, stdout=open_vcf, stderr=log)
elapsed_time = divmod(
(datetime.datetime.now() - start_time).total_seconds(), 60)
open_vcf.close()
if not success:
print("- VarScan mpileup2indel: %d min, %d sec" % elapsed_time)
return vcf
else:
f.prRed('Error in VarScan mpileup2indel. Check log file.')
exit(1)
def Concat_VarScan_vcf(snp, indel, log):
concat = '.'.join(snp.split('.')[:-2] + ['merge.vcf'])
open_concat = open(concat, 'w')
sort = '.'.join(concat.split('.')[:-1] + ['sort.vcf'])
open_sort = open(sort, 'w')
args = ['bgzip', snp]
status = subprocess.call('bgzip -f ' + snp, shell=True)
status = subprocess.call('tabix -f ' + snp + '.gz', shell=True)
status = subprocess.call('bgzip -f ' + indel, shell=True)
status = subprocess.call('tabix -f ' + indel + '.gz', shell=True)
args = ['vcf-concat', snp + '.gz', indel + '.gz']
success1 = subprocess.call(args, stdout=open_concat, stderr=log)
args = ['vcf-sort', '-c', concat]
success2 = subprocess.call(args, stdout=open_sort, stderr=log)
if success1 or success2:
f.prRed('Error in VarScan concat. Check log file.')
exit(1)
else:
return sort
def Index_vcf(path, vcf, log):
args = [path, 'IndexFeatureFile', '-F', vcf]
success = subprocess.call(args, stdout=log, stderr=log)
if not success:
pass
else:
f.prRed('Error in Index Vcf. Check log file.')
exit(1)
def Mutect2(path, ram, gbam, sbam, gsample_name, ssample_name, reference,
target, log, workdir):
start_time = datetime.datetime.now()
vcf = workdir + '/' + ssample_name + '.Mutect.vcf'
filtered_vcf = workdir + '/' + ssample_name + '.Mutect.filter.vcf'
version = check_version_gatk(path, log)
if version.startswith('3'):
if gbam == None:
args = [
'java', '-Xmx' + ram, '-jar', path, '-T', 'MuTect2', '-R',
reference, '-I:tumor', sbam, '-o', vcf
]
else:
args = [
'java', '-Xmx' + ram, '-jar', path, '-T', 'MuTect2', '-R',
reference, '-I:tumor', sbam, '-I:normal', gbam, '-o', vcf
]
if version.startswith('4.1'):
if gbam == None:
args = [
path, 'Mutect2', '-R', reference, '-I', sbam, '-tumor',
ssample_name, '--max-reads-per-alignment-start', '0', '-O', vcf
]
else:
args = [
path, 'Mutect2', '-R', reference, '-I', sbam, '-tumor',
ssample_name, '-I', gbam, '-normal', gsample_name,
'--max-reads-per-alignment-start', '0', '-O', vcf
]
if target != None:
args += ['-L', target]
#success = subprocess.call(args)
success = subprocess.call(args, stdout=log, stderr=log)
args = [
path, 'FilterMutectCalls', '-R', reference, '-V', vcf, '-O',
filtered_vcf
]
success = subprocess.call(args, stdout=log, stderr=log)
elapsed_time = divmod(
(datetime.datetime.now() - start_time).total_seconds(), 60)
if not success:
print("- " + ssample_name + ": %d min, %d sec" % elapsed_time)
return filtered_vcf
else:
f.prRed('Error in Mutect2. Check log file.')
exit(1)
def header_fix(path, vcf, variantcaller, log):
fix_vcf = '.'.join(vcf.split('.')[:-1] + ['hfix.vcf'])
open_fix_vcf = open(fix_vcf, 'w')
args = ['python2', path, '-v', variantcaller, '-f', vcf]
success = subprocess.call(args, stdout=open_fix_vcf, stderr=log)
open_fix_vcf.close()
if not success:
return fix_vcf
else:
f.prRed('Error in Vcf fix. Check log file.')
exit(1)
def vcf_norm(path, vcf, reference, log):
norm_vcf = '.'.join(vcf.split('.')[:-1] + ['norm.vcf'])
args = [
path, 'norm', '-D', '-m', '-both', '-f', reference, vcf, '-o', norm_vcf
]
success = subprocess.call(args, stdout=log, stderr=log)
if not success:
return norm_vcf
else:
f.prRed('Error in Vcf normalization. Check log file.')
exit(1)
def SamFormatConverter(path, ram, sam, log, workdir):
bam = workdir + '/' + '.'.join(sam.split('/')[-1].split('.')[:-1]) + '.bam'
args = [
'java', '-Xmx' + ram, '-jar', path, 'SamFormatConverter', 'I=' + sam,
'O=' + bam
]
success = subprocess.call(args, stdout=log, stderr=log)
if not success:
return bam
else:
f.prRed('Error in Conversion. Check log file.')
exit(1)
def merge_vcf(path, name, gatk, freebayes, varscan, log, workdir):
merge_vcf = workdir + '/' + name + '.merge.vcf'
args = ['python2', path, '-g', gatk, '-f', freebayes, '-o', merge_vcf]
if varscan:
args += ['-v', varscan]
success = subprocess.call(args, stdout=log, stderr=log)
if not success:
return merge_vcf
else:
f.prRed('Error in Vcf merging. Check log file.')
exit(1)
def LeftAlignAndTrimVariants(path, vcf, reference, log):
norm_vcf = '.'.join(vcf.split('.')[:-1] + ['norm.vcf'])
args = [
path, 'LeftAlignAndTrimVariants', '-R', reference, '-V', vcf, '-O',
norm_vcf, '--split-multi-allelics'
]
success = subprocess.call(args, stdout=log, stderr=log)
if not success:
return norm_vcf
else:
f.prRed(
'Error in Vcf LeftAlignAndTrimVariants normalization. Check log file.'
)
exit(1)
def SortSam(path, ram, bam, log, workdir):
#print('- Bam sorting')
sort = workdir + '/' + '.'.join(
bam.split('/')[-1].split('.')[:-1]) + '.sort.bam'
args = [
'java', '-Xmx' + ram, '-jar', path, 'SortSam', 'I=' + bam, 'O=' + sort,
'SORT_ORDER=coordinate'
]
success = subprocess.call(args, stdout=log, stderr=log)
if not success:
return sort
else:
f.prRed('Error in Sorting. Check log file.')
exit(1)
def add_Annotation(path, name, vcf, tsv, tag_list, transcript_list, log,
workdir):
annotated_tsv = workdir + '/' + name + '.tsv'
args = [
'python2', path, '--vcf', vcf, '--tsv', tsv, '-o', annotated_tsv,
'--tag_list', tag_list, '--trs_list', transcript_list
]
success = subprocess.call(args, stdout=log, stderr=log)
if success:
f.prRed('Error in tsv annotation. Check log file.')
exit(1)
return annotated_tsv
def LocatIt(path, ram, bam, fqI2, log, workdir):
#print("- Merging haloplex molecular barcodes")
outbam = workdir + '/' + '.'.join(
sam.split('/')[-1].split('.')[:-1] + ['MCBmerged'] + ['bam'])
args = [
'java', '-Xmx' + ram, '-jar', path, '-U', '-IB', '-OB', '-i', '-o',
outbam, bam, fqI2
]
success = subprocess.call(args, stdout=log, stderr=log)
if not success:
return outbam
else:
f.prRed('Error in merging molucular barcodes. Check log file.')
exit(1)
def BuildBamIndex(path, ram, bam, log):
#print('- Bam indexing')
bai = bam + '.bai'
if os.path.exists(bai):
status = subprocess.call("rm " + bai, shell=True)
args = [
'java', '-Xmx' + ram, '-jar', path, 'BuildBamIndex', 'I=' + bam,
'O=' + bai, 'VALIDATION_STRINGENCY=LENIENT'
]
success = subprocess.call(args, stdout=log, stderr=log)
if not success:
pass
else:
f.prRed('Error in Indexing. Check log file.')
exit(1)
def HardFilter(path, ram, vcf, sample_name, reference, target, log, workdir):
start_time = datetime.datetime.now()
vcf_filtered = workdir + '/' + '.'.join(
vcf.split('/')[-1].split('.')[:-1] + ['FILTER.vcf'])
version = check_version_gatk(path, log)
if version.startswith('3'):
args = [
'java', '-Xmx' + ram, '-jar', path, '-T', 'VariantFiltration',
'-V', vcf, '-R', reference, '-o', vcf_filtered
]
elif version.startswith('4.1'):
args = [
path, 'VariantFiltration', '-R', reference, '-V', vcf, '-O',
vcf_filtered
]
if 'FreeBayes' in vcf:
pass
#args += ['--filter-name','Low-AD','--filter-expression',"AO < 20" ]
#args += ['--filter-name','Low-MapQual','--filter-expression',"MQM < 40.0"]
else:
#args += ['--filter-name','Low-Qual','--filter-expression',"QD < 2.0"]
#args += ['--filter-name','High-FS','--filter-expression',"FS > 60.0"]
#args += ['--filter-name','High-SOR','--filter-expression',"SOR > 3.0"]
#args += ['--filter-name','Low-MapQual','--filter-expression',"MQ < 40.0"]
args += [
'--filter-name', 'LOW-MQMQRS', '--filter-expression',
"MQRankSum < -2.5"
]
args += [
'--filter-name', 'HIGH-RPOS', '--filter-expression',
"ReadPosRankSum < -8.0 || ReadPosRankSum > 8.0 "
]
success = subprocess.call(args, stdout=log, stderr=log)
#success = 0
elapsed_time = divmod(
(datetime.datetime.now() - start_time).total_seconds(), 60)
if not success:
#print("- CombineGVCFs " +sample_name + ": %d min, %d sec" % elapsed_time)
return vcf_filtered
else:
f.prRed('Error in HardFiltering: ' + sample_name + '. Check log file.')
exit(1)
def Decon_makeCNVcalls(path, rdata, sample_name, reference, log, workdir):
out = workdir + '/' + sample_name + '.DECON.CNV'
args = [
'Rscript', './makeCNVcalls.R', '--Rdata', rdata, '--transProb', '0.01',
'--out', out
]
success = subprocess.call(args, stdout=log, stderr=log)
calls = out + '_all.txt'
#success = False
if not success:
#print("- Estraction: %d min, %d sec" % elapsed_time)
return calls
else:
f.prRed('Error in DECON CNV calling. Check log file.')
exit(1)
def Decon_ReadInBams(path, bam_list, sample_name, target_bed, reference, log,
workdir):
out = workdir + '/' + sample_name
args = [
'Rscript', './ReadInBams.R', '--bams', bam_list, '--bed', target_bed,
'--fasta', reference, '--out', out
]
success = subprocess.call(args, stdout=log, stderr=log)
rdata = out + '.RData'
#success = False
if not success:
#print("- Estraction: %d min, %d sec" % elapsed_time)
return rdata
else:
f.prRed('Error in DECON CNV calling. Check log file.')
exit(1)
def GATK_CollectReadCounts(path, ram, bam, sample_name, target_list, log,
workdir):
success = False
version = check_version_gatk(path, log)
hdf5 = workdir + '/' + sample_name + '.hdf5'
if version.startswith('4.1'):
args = [
path, 'CollectReadCounts', '-I', bam, '-L', target_list,
'--interval-merging-rule', 'OVERLAPPING_ONLY', '-O', hdf5
]
success = subprocess.call(args, stdout=log, stderr=log)
subprocess.call(['/bin/bash', '-i', '-c', "conda deactivate"])
if not success:
#print("- Estraction: %d min, %d sec" % elapsed_time)
return hdf5
else:
f.prRed('Error in CNV calling. Check log file.')
exit(1)
def Sort_vcf(path, vcf, log, workdir):
sorted_vcf = '.'.join(vcf.split('.')[:-1] + ['sort.vcf'])
open_sorted_vcf = open(sorted_vcf, 'w')
args = ['vcf-sort', vcf]
success = subprocess.call(args, stdout=open_sorted_vcf, stderr=log)
open_sorted_vcf.close()
args = ['bgzip', sorted_vcf, '-f', '>', sorted_vcf + '.gz']
success = subprocess.call(args, stdout=log, stderr=log)
args = ['tabix', '-p', 'vcf', sorted_vcf + '.gz']
success = subprocess.call(args, stdout=log, stderr=log)
if not success:
return sorted_vcf + '.gz'
else:
f.prRed('Error in Vcf Sorting. Check log file.')
exit(1)
def MarkDuplicates(path, ram, bam, log, workdir):
#print("- Marking duplicates")
outbam = workdir + '/' + '.'.join(
bam.split('/')[-1].split('.')[:-1] + ['Mark'] + ['bam'])
metrics_file = workdir + '/' + '.'.join(
bam.split('/')[-1].split('.')[:-1] + ['MarkMetrics'] + ['txt'])
args = [
'java', '-Xmx' + ram, '-jar', path, 'MarkDuplicates', 'I=' + bam,
'O=' + outbam, 'METRICS_FILE=' + metrics_file, 'READ_NAME_REGEX=null',
'ASSUME_SORTED=true', 'VALIDATION_STRINGENCY=LENIENT'
]
success = subprocess.call(args, stdout=log, stderr=log)
if not success:
return outbam
else:
f.prRed('Error in Marking of duplicates. Check log file.')
exit(1)
def AddOrReplaceReadGroups(path, ram, bam, sample_name, panel, run, log,
workdir):
#print("- Add/replace Read groups")
outbam = workdir + '/' + '.'.join(
bam.split('/')[-1].split('.')[:-1] + ['RG'] + ['bam'])
args = [
'java', '-Xmx' + ram, '-jar', path, 'AddOrReplaceReadGroups',
'I=' + bam, 'O=' + outbam, 'RGID=' + sample_name, 'RGPL=ILLUMINA',
'RGSM=' + sample_name, 'RGLB=' + panel, "RGPU=" + run,
'VALIDATION_STRINGENCY=LENIENT'
]
success = subprocess.call(args, stdout=log, stderr=log)
if not success:
return outbam
else:
f.prRed('Error in Adding or replacing Read groups. Check log file.')
exit(1)
