Adds AD=2 to VCF on a stream

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='')