number of SNPs per sample in multi-sample VCF file
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
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it should be
nNonRefHomisn't it ?What's the ploidy of your samples? I would argue SNP count should be
nNonRefHomandnHetssince heterozygote SNPs are still informative in most cases so long as your samples are at least diploid.