filter vcf to include only sites which have at least one homozygous alt call

Question

[grey]

Hi all,

I am trying to extract a subset of sites from a multi-sample vcf file. I only want those sites with at least one homozygous alternative allele call. Some sites are poly-allelic so sites that I want would have at least one 1/1 or 2/2 call.

I've looked through bcftools, vcftools, but haven't found an elegant solution. For example, from the documentation it seems bcftools --genotype can filter for sites with at least one homozygous call, but these could be ref or alt, and I want specifically alt calls.

Any ideas would be greatly appreciated!

[Sunnywy0808]

You mentioned that "Some sites are poly-allelic." I’d like to ask, how are such sites represented in a VCF file? Does "poly-allelic" correspond to "biallelic sites"?

Answer 1

[Pierre Lindenbaum]

 bcftools view -i 'N_PASS(GT="AA")>=1'  in.vcf

not tested: I don't know if it will accept 1/2 genotypes too.

[finswimmer]

bcftools view -i 'GT="AA"' in.vcf should be enough, as the manual differs between AA (alt-alt hom) and Aa/aA (alt-alt het)

[grey]

Works perfect thank you