Hello, I have some questions about this filter.I work with WES so :

vcftolls --min-alleles 2 --max-alleles 2 --recode --out

1. I understand that it is used to maintain only biallelic sites, but what is the reason for maintaining only these types of variants? Is it because multi-allelic variants are rare and you are more likely to be able to get a false positive call? Or is it because from the analysis of the child population it is better to have 2 alleles in ref and in alternative changes?

2. I applied this filter and it doesn't remove anything. The variants keep the same set, why? Is the fact that I don't have multi-allelic sites in my set available?

Thank you, I appreciate all your clarifications.