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

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,

bcftools vcftools
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written by kumar.vinod81 kumar.vinod81

1 answer

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

bcftools stats -i"GT='het'" in.bcf
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written by 4galaxy77 4galaxy77

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,

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written by kumar.vinod81 kumar.vinod81

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