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stephenturner/addad.py

Created June 23, 2022 11:33
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Adds AD=2 to VCF on a stream
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addad.py
#!/usr/bin/env python
# Adds allelic depth (AD)=2 to a VCF.
# Usage: bcftools view my.vcf.gz | addad.py | bcftools sort -Oz -o my.ad.vcf.gz && tabix my.ad.vcf.gz
import pysam
vcf_in=pysam.VariantFile("-","r")
vcf_in.header.formats.add("AD",".","Integer","Allelic depth, hard-coded as 2")
print(vcf_in.header, end='')
for variant in vcf_in:
for sample in variant.samples:
variant.samples[sample]['AD']=2
print(variant, end='')
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