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Do not write variants below --allele_freq_thres to .vcf file #4

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Do not write variants below --allele_freq_thres to .vcf file #4

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7 changes: 5 additions & 2 deletions bin/type_vcf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ def parse_args(args=None):

return parser.parse_args(args)

def ivar_variants_to_vcf_string(FileIn,RefIn):
def ivar_variants_to_vcf_string(FileIn,RefIn,minAF):
'''
Credit to nf-core: https://github.com/nf-core/viralrecon

Expand Down Expand Up @@ -77,6 +77,7 @@ def ivar_variants_to_vcf_string(FileIn,RefIn):
ID='.'
REF=line[2]
ALT=line[3]
ALT_FREQ=line[10]
var_type = 'SNP'
if ALT[0] == '+':
ALT = REF + ALT[1:]
Expand All @@ -98,6 +99,8 @@ def ivar_variants_to_vcf_string(FileIn,RefIn):
writeLine = True
if (CHROM,POS,REF,ALT) in varList:
writeLine = False
if float(ALT_FREQ) < minAF:
writeLine = False
if re.match('^.*N+$', REF):
writeLine = False
else:
Expand Down Expand Up @@ -348,7 +351,7 @@ def main(args=None):
args = parse_args(args)

if args.TSV_IN:
vcfString = ivar_variants_to_vcf_string(args.TSV_IN,args.REF_IN)
vcfString = ivar_variants_to_vcf_string(args.TSV_IN,args.REF_IN,args.ALLELE_FREQ_THRESH)

elif args.VCF_IN:
vcfString = read_vcf_to_vcf_string(args.VCF_IN)
Expand Down