Dear all,

I am new to SNP-calling. I am trying to find a quick way to count how missing genotypes (./.) I have each sample in my vcf file.

I also want to count stats per variant. In each position that an SNP is found in one sample, what would other samples look like? For example, in the same position, one sample might have a missing value while in another insertion or deletion.

Could you help me if plink2 can answer my questions or any other program you know of? I have heard of bcftools, but it is not so fas as plink2

Thank you for your time