def runMutectReverse(infiles, outfile):
'''Use control as tumor and vis versa to estimate false positive rate'''
infile, normal_panel = infiles
infile_tumour = infile.replace(PARAMS["sample_control"],
PARAMS["sample_tumour"])
basename = P.snip(outfile, "_normal_mutect.vcf")
call_stats_out = basename + "_call_stats.out"
mutect_log = basename + ".log"
basename = P.snip(outfile, ".mutect.reverse.snp.vcf")
call_stats_out = basename + "_call_stats.reverse.out"
coverage_wig_out = basename + "_coverage.reverse.wig"
mutect_log = basename + ".reverse.log"
(cosmic, dbsnp, quality, max_alt_qual, max_alt, max_fraction,
tumor_LOD) = (PARAMS["mutect_cosmic"], PARAMS["gatk_dbsnp"],
PARAMS["mutect_quality"], PARAMS["mutect_max_alt_qual"],
PARAMS["mutect_max_alt"], PARAMS["mutect_max_fraction"],
PARAMS["mutect_LOD"])
genome = "%s/%s.fa" % (PARAMS["bwa_index_dir"], PARAMS["genome"])
PipelineExome.mutectSNPCaller(infile, outfile, mutect_log, genome, cosmic,
dbsnp, call_stats_out,
PARAMS['mutect_memory'],
PARAMS['mutect_threads'], quality,
max_alt_qual, max_alt, max_fraction,
tumor_LOD, normal_panel, infile_tumour)
def runMutectOnDownsampled(infiles, outfile):
'''call somatic SNPs using MuTect on downsampled bams'''
infile, normal_panel = infiles
infile_tumour = infile.replace(
PARAMS["sample_control"], PARAMS["sample_tumour"])
basename = P.snip(outfile, "_normal_mutect.vcf")
call_stats_out = basename + "_call_stats.out"
mutect_log = basename + ".log"
(cosmic, dbsnp, quality, max_alt_qual, max_alt,
max_fraction, tumor_LOD) = (
PARAMS["mutect_cosmic"], PARAMS["gatk_dbsnp"],
PARAMS["mutect_quality"], PARAMS["mutect_max_alt_qual"],
PARAMS["mutect_max_alt"], PARAMS["mutect_max_fraction"],
PARAMS["mutect_LOD"])
genome = "%s/%s.fa" % (PARAMS["bwa_index_dir"],
PARAMS["genome"])
PipelineExome.mutectSNPCaller(infile_tumour, outfile, mutect_log, genome,
cosmic, dbsnp, call_stats_out,
PARAMS['mutect_memory'], PARAMS['mutect_threads'],
quality, max_alt_qual,
max_alt, max_fraction, tumor_LOD,
normal_panel, infile)
def runMutectReverse(infiles, outfile):
'''Use control as tumor and vis versa to estimate false positive rate'''
infile, normal_panel = infiles
infile_tumour = infile.replace(
PARAMS["sample_control"], PARAMS["sample_tumour"])
basename = P.snip(outfile, "_normal_mutect.vcf")
call_stats_out = basename + "_call_stats.out"
mutect_log = basename + ".log"
basename = P.snip(outfile, ".mutect.reverse.snp.vcf")
call_stats_out = basename + "_call_stats.reverse.out"
coverage_wig_out = basename + "_coverage.reverse.wig"
mutect_log = basename + ".reverse.log"
(cosmic, dbsnp, quality, max_alt_qual, max_alt,
max_fraction, tumor_LOD) = (
PARAMS["mutect_cosmic"], PARAMS["gatk_dbsnp"],
PARAMS["mutect_quality"], PARAMS["mutect_max_alt_qual"],
PARAMS["mutect_max_alt"], PARAMS["mutect_max_fraction"],
PARAMS["mutect_LOD"])
genome = "%s/%s.fa" % (PARAMS["bwa_index_dir"],
PARAMS["genome"])
PipelineExome.mutectSNPCaller(infile, outfile, mutect_log, genome,
cosmic, dbsnp, call_stats_out,
PARAMS['mutect_memory'],
PARAMS['mutect_threads'],
quality, max_alt_qual,
max_alt, max_fraction, tumor_LOD,
normal_panel, infile_tumour)
def callControlVariants(infile, outfile):
'''run mutect to call snps in control sample'''
basename = P.snip(outfile, "_normal_mutect.vcf")
call_stats_out = basename + "_call_stats.out"
mutect_log = basename + ".log"
cosmic, dbsnp, = (PARAMS["mutect_cosmic"],
PARAMS["gatk_dbsnp"])
genome = "%s/%s.fa" % (PARAMS["bwa_index_dir"],
PARAMS["genome"])
PipelineExome.mutectSNPCaller(infile, outfile, mutect_log, genome, cosmic,
dbsnp, call_stats_out, PARAMS['mutect_memory'],
PARAMS['mutect_threads'], artifact=True)
def callControlVariants(infile, outfile):
'''run mutect to call snps in control sample'''
basename = P.snip(outfile, "_normal_mutect.vcf")
call_stats_out = basename + "_call_stats.out"
mutect_log = basename + ".log"
cosmic, dbsnp, = (PARAMS["mutect_cosmic"], PARAMS["gatk_dbsnp"])
genome = "%s/%s.fa" % (PARAMS["bwa_index_dir"], PARAMS["genome"])
PipelineExome.mutectSNPCaller(infile,
outfile,
mutect_log,
genome,
cosmic,
dbsnp,
call_stats_out,
PARAMS['mutect_memory'],
PARAMS['mutect_threads'],
artifact=True)
def runMutectOnDownsampled(infiles, outfile):
'''call somatic SNPs using MuTect on downsampled bams'''
infile, normal_panel = infiles
infile_tumour = infile.replace(PARAMS["sample_control"],
PARAMS["sample_tumour"])
basename = P.snip(outfile, "_normal_mutect.vcf")
call_stats_out = basename + "_call_stats.out"
mutect_log = basename + ".log"
(cosmic, dbsnp, quality, max_alt_qual, max_alt, max_fraction,
tumor_LOD) = (PARAMS["mutect_cosmic"], PARAMS["gatk_dbsnp"],
PARAMS["mutect_quality"], PARAMS["mutect_max_alt_qual"],
PARAMS["mutect_max_alt"], PARAMS["mutect_max_fraction"],
PARAMS["mutect_LOD"])
genome = "%s/%s.fa" % (PARAMS["bwa_index_dir"], PARAMS["genome"])
PipelineExome.mutectSNPCaller(infile_tumour, outfile, mutect_log, genome,
cosmic, dbsnp, call_stats_out,
PARAMS['mutect_memory'],
PARAMS['mutect_threads'], quality,
max_alt_qual, max_alt, max_fraction,
tumor_LOD, normal_panel, infile)