How to filter allele frequency of each sample with different Zygosity status (exclude likely non-germline variants)

Question

[YL]

Hello,

I have a multiple sample VCF file and I have to exclude likely non-germline variants based on allele frequency (AF). For example, allele A in Sample X was called as 0/1 but only with AF 25%, so I want to set the genotype of allele A in sample X to "./.".

just as what it dose for this webpage: https://www.goldenhelix.com/learning/knowledge-base/svs-introduction-to-ngs-tutorial/#3-quality-filters search "Zygosity Based Filtering"

The ultimate goal is to convert my vcf file to a genotype matrix. So if there is a way to do this filter in a genotype matrix format, it would also be great.

Thank you very much!

Answer 1

[YL]

I learned how to do it from this thread: Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4