number of SNPs per sample in multi-sample VCF file

Question

[reza]

I run following command on my multi-sample vcf file including 10 samples

bcftools stats --samples "-" in.vcf.gz

in a part of output, there are a table with following column titles

PSC [2]id   [3]sample   [4]nRefHom  [5]nNonRefHom   [6]nHets    [7]nTransitions [8]nTransversions   [9]nIndels  [10]average depth   [11]nSingletons [12]nHapRef [13]nHapAlt [14]nMissing

sum of which columns is SNP count for each sample.

Thanks

[Pierre Lindenbaum]

it should be nNonRefHom isn't it ?

[dthorbur]

What's the ploidy of your samples? I would argue SNP count should be nNonRefHom and nHets since heterozygote SNPs are still informative in most cases so long as your samples are at least diploid.