I have a bunch of variants in .VCF file which I got through the unified genotyper tool. Now I want to filter only the "Homozygous" (100% alternate allele frequency) variants. But the Snpsift filter and SnpEff tools do not have any option to change what on basis the variants are annotated as "Homozygous" and Heterozygous". At least is there are way to filter out the variants based on frequency of alternate non-reference alleles.
In my case I need only the variants with 100% of alternate non-reference alleles. Can someone help me on this?. It would be a great help.
Thanks in Advance.