Checking reads

bcftools query -i 'GT="AA"' \ -f '%CHROM\t%POS\t%REF\t%ALT[\t%AD]\n' sample.vcf.gz \ | awk -F'\t' '{split($5,a,","); af=a[2]/(a[1]+a[2]); if (af < 0.85) print $0 "\t" af}' This prints every "homozygous" call where fewer than 85% of reads support the alternate allele. For older samtools-style VCFs without AD, compute the fraction from INFO/DP4 instead: (alt-fwd + alt-rev) / total.