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