def run(args):
'''Main wrapper function for filtering MuTect VCF files'''
logger.info('<FILTER>LowDPN=Normal depth < {0.min_normal_depth}'.format(args))
logger.info('<FILTER>LowDPT=Tumor depth < {0.min_tumor_depth}'.format(args))
logger.info('<FILTER>TAF=(SAMPLE == TUMOR) && (TYPE==SOM) && AF < {0.min_alt_freq_tumor:.2f}'.format(args))
logger.info('<FILTER>NAF=(SAMPLE == NORMAL) && (TYPE==SOM) && AF >= {0.max_alt_freq_normal:.2f}'.format(args))
logger.info('<FILTER>LowBQ=BQ < {0.min_base_quality}'.format(args))
# New filter and info lines to add to the output vcf
filters = [
'##FILTER=<ID=LowDPN,Description="Normal depth < {0.min_normal_depth}">'.format(args),
'##FILTER=<ID=LowDPT,Description="Tumor depth < {0.min_tumor_depth}">'.format(args),
'##FILTER=<ID=TAF,Description="Tumor: (TYPE == SOM) && AF < {0.min_alt_freq_tumor:.2f}">'.format(args),
'##FILTER=<ID=NAF,Description="Normal: (TYPE == SOM) && AF >= {0.max_alt_freq_normal:.2f}">'.format(args),
'##FILTER=<ID=LowBQ,Description="BQ < {0.min_base_quality}">'.format(args),
'##FILTER=<ID=UK,Description="SS==5">'
]
info = [
'##INFO=<ID=NTYPE,Number=1,Type=String,Description="Normal type, can be WT, GERM, SOMATIC, LOH, PTM, UK">',
'##INFO=<ID=TTYPE,Number=1,Type=String,Description="Tumor type, can be WT, GERM, SOMATIC, LOH, PTM, UK">'
]
# Process the file
with open(args.output_vcf, 'wb') as o:
mutect_reader = VcfReader(args.choice, args.tumor_name, args.normal_name, args.input_vcf)
mutect_reader.Open()
mutect_reader.get_header()
mutect_reader.write_new_header(o, filters=filters, info=info)
mutect_reader.apply_filters(o, args, MutectRecord)
mutect_reader.Close()
def run(args):
'''Main wrapper function for filtering SomaticSniper VCF files'''
# Print the filters to the log
logger.info(
'<FILTER>LowDPN="Normal DP < {0.min_normal_depth}"'.format(args))
logger.info('<FILTER>LowDPT="Tumor DP < {0.min_tumor_depth}"'.format(args))
logger.info('<FILTER>LowMQT="Tumor MQ < {0.min_mapq_tumor}"'.format(args))
logger.info(
'<FILTER>LowMQN="Normal MQ < {0.min_mapq_normal}"'.format(args))
logger.info('<FILTER>LowGQT="Tumor GQ < {0.min_gq_tumor}"'.format(args))
logger.info('<FILTER>LowGQN="Normal GQ < {0.min_gq_normal}"'.format(args))
logger.info(
'<FILTER>LowScore="Somatic score < {0.min_somatic_score}"'.format(
args))
# New info and filter lines
info = [
'##INFO=<ID=NTYPE,Number=1,Type=String,Description="Normal type, can be REF,GERM,SOMATIC,LOH,UK">',
'##INFO=<ID=TTYPE,Number=1,Type=String,Description="Tumor type REF,GERM,SOMATIC,LOH,UK">'
]
filters = [
'##FILTER=<ID=PASS,Description="Accept as a confident somatic mutation">',
'##FILTER=<ID=LowDPN,Description="Normal DP < {0.min_normal_depth}">'.
format(args),
'##FILTER=<ID=LowDPT,Description="Tumor DP < {0.min_tumor_depth}">'.
format(args),
'##FILTER=<ID=LowMQT,Description="Tumor MQ < {0.min_mapq_tumor}">'.
format(args),
'##FILTER=<ID=LowMQN,Description="Normal MQ < {0.min_mapq_normal}">'.
format(args),
'##FILTER=<ID=LowGQT,Description="Tumor GQ < {0.min_gq_tumor}">'.
format(args),
'##FILTER=<ID=LowGQN,Description="Normal GQ < {0.min_gq_normal}">'.
format(args),
'##FILTER=<ID=LowScore,Description="Somatic score < {0.min_somatic_score}">'
.format(args), '##FILTER=<ID=UK,Description="Unknown variant type">'
]
# Load the contigs
contigs = load_contigs(args)
# Process the file
with open(args.output_vcf, 'wb') as o:
sniper_reader = VcfReader(args.choice, args.tumor_name,
args.normal_name, args.input_vcf)
sniper_reader.Open()
sniper_reader.get_header()
sniper_reader.write_new_header(o,
filters=filters,
info=info,
contigs=contigs)
sniper_reader.apply_filters(o, args, SniperRecord)
sniper_reader.Close()
logger.info('Filtered and formatted VCF file: {0}'.format(
os.path.abspath(args.output_vcf)))
def run(args):
'''Main wrapper function for filtering MuTect VCF files'''
logger.info(
'<FILTER>LowDPN=Normal depth < {0.min_normal_depth}'.format(args))
logger.info(
'<FILTER>LowDPT=Tumor depth < {0.min_tumor_depth}'.format(args))
logger.info(
'<FILTER>TAF=(SAMPLE == TUMOR) && (TYPE==SOM) && AF < {0.min_alt_freq_tumor:.2f}'
.format(args))
logger.info(
'<FILTER>NAF=(SAMPLE == NORMAL) && (TYPE==SOM) && AF >= {0.max_alt_freq_normal:.2f}'
.format(args))
logger.info('<FILTER>LowBQ=BQ < {0.min_base_quality}'.format(args))
# New filter and info lines to add to the output vcf
filters = [
'##FILTER=<ID=LowDPN,Description="Normal depth < {0.min_normal_depth}">'
.format(args),
'##FILTER=<ID=LowDPT,Description="Tumor depth < {0.min_tumor_depth}">'.
format(args),
'##FILTER=<ID=TAF,Description="Tumor: (TYPE == SOM) && AF < {0.min_alt_freq_tumor:.2f}">'
.format(args),
'##FILTER=<ID=NAF,Description="Normal: (TYPE == SOM) && AF >= {0.max_alt_freq_normal:.2f}">'
.format(args),
'##FILTER=<ID=LowBQ,Description="BQ < {0.min_base_quality}">'.format(
args), '##FILTER=<ID=UK,Description="SS==5">'
]
info = [
'##INFO=<ID=NTYPE,Number=1,Type=String,Description="Normal type, can be WT, GERM, SOMATIC, LOH, PTM, UK">',
'##INFO=<ID=TTYPE,Number=1,Type=String,Description="Tumor type, can be WT, GERM, SOMATIC, LOH, PTM, UK">'
]
# Process the file
with open(args.output_vcf, 'wb') as o:
mutect_reader = VcfReader(args.choice, args.tumor_name,
args.normal_name, args.input_vcf)
mutect_reader.Open()
mutect_reader.get_header()
mutect_reader.write_new_header(o, filters=filters, info=info)
mutect_reader.apply_filters(o, args, MutectRecord)
mutect_reader.Close()
def run(args):
'''Main wrapper function for filtering Shimmer VCF files'''
# Print the filters to the log
logger.info('<FILTER>LowDPN=Normal DP < {0.min_normal_depth}'.format(args))
logger.info('<FILTER>LowDPT=Tumor DP < {0.min_tumor_depth}'.format(args))
logger.info('<FILTER>TAF=Tumor AF < {0.min_alt_freq_tumor:.3f}>'.format(args))
logger.info('<FILTER>NAF=Normal AF >= {0.max_alt_freq_normal:.3f}>'.format(args))
logger.info('<FILTER>LowQual=QUAL < {0.min_qual}>'.format(args))
# New filter and format lines
formats = ['##FORMAT=<ID=AF,Number=1,Type=Float,Description="Ratio of reads with alternate base">']
filters = [
'##FILTER=<ID=PASS,Description="Accept as a confident somatic mutation">',
'##FILTER=<ID=LowDPN,Description="Normal DP < {0.min_normal_depth}">'.format(args),
'##FILTER=<ID=LowDPT,Description="Tumor DP < {0.min_tumor_depth}">'.format(args),
'##FILTER=<ID=TAF,Description="Tumor AF < {0.min_alt_freq_tumor:.3f}">'.format(args),
'##FILTER=<ID=NAF,Description="Normal AF >= {0.max_alt_freq_normal:.3f}">'.format(args),
'##FILTER=<ID=LowQual,Description="QUAL < {0.min_qual}">'.format(args)
]
# Load the VarSifter dictionary
varsifter = load_varsifter(args)
# Load the contigs
reffile = '##reference=file://' + os.path.abspath(args.reference)
contigs = load_contigs(args)
# Process the file
with open(args.output_vcf, 'wb') as o:
shimmer_reader = VcfReader(args.choice, args.tumor_name, args.normal_name, args.input_vcf)
shimmer_reader.Open()
shimmer_reader.get_header()
shimmer_reader.write_new_header(o, filters=filters, formats=formats,
refpath=reffile, contigs=contigs)
shimmer_reader.apply_filters(o, args, ShimmerRecord, vsdict=varsifter)
shimmer_reader.Close()
