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 highly heterozygous plant species generated from GATK, and I could do many things like stats and filters with vcftools and bcftools.
I could calculate the individual-wise heterozygosity using -het option in vcftools. But I am also interested in frequency of heterozygous SNPs in my data for all the SNPs. And then to filter out some SNPs which are highly heterozygous.
Is it possible with vcftools or bcftools?
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