I wanted to say that I have analyze my NGS data and now I have a sheet of my variants along with their Allele frequencies in each of my sample (from VCF and Bam files).
I wanted to ask what threshold of Allele frequency should I set to pick my good quality variants? e.g. some people say that if Allele frequency in VCF file is more than 20% in VCF file it means your Variant is of good quality. Also what threshold people set for variant calling.
Can someone help me please.