How to calculate frequency of heterozygous SNPs in multisample VCF file and to filter out over a specific range?

Question

[kumar.vinod81]

Hi, I've a multi-sample vcf file of a highly heterozygous plant species. I could calculate the individual-wise heterozygosity using -het option in vcftools. But I also want to know the frequency of heterozygous SNPs in my data. And then to filter out some SNPs where the frequency of heterozygous allele is > 50% and in another filter I want to keep only those SNPs where minor homozygous allele count is >3. Is it possible with vcftools or bcftools? Thanks,

Answer 1

[4galaxy77]

Not 100% sure what you need, but try something like this (not tested)

bcftools stats -i"GT='het'" in.bcf

[kumar.vinod81]

But is it possible to filter with allele count? I want to filter out all the sites having >3 het or want to include only sites with >2 homozygous alleles. Thanks,