How does vcf-stats give snp count

Question

[Saad Khan]

Hi

I was wondering if the snp-count that vcf-stats gives includes homozygous reference counts as well. Its my understanding that homozygous refernce nucleotides would not be SNPs and I was not sure about vcf-stats as it is thin on documentation so just wanted to confirm.

[iraun]

I've never used vcf-stats, but I would say that yes, it includes homozygous reference alleles. Just think that if you have more than one sample, it is interesting to know for a given SNP, if one sample is heterozygous/homo for the alt, and the other homo for the ref. But as I've told you, I've never used this tool. But, furthermore, reading this thread (Vcftools Vcf-Stats Field Definitions), it seems also that it actually counts homo ref alleles.