This is a test version of Biostars. For the public version, visit https://www.biostars.org.
What is the meaning of the terms output by vcf-stats?

After running vcf-stats on a vcf file I get terms like:

'snp_count',
'private',
'hom_AA_count',
'hom_RR_count',
'ref_count',
'count',
'unphased',
'het_RA_count',
'ref',
'indel_count'

snp_count should be the number of snps, and indel_count is the number of indels. Private from googling appears to be number of SNPs (or maybe variants) exclusive to a sample in a multi-sample SNP. However, what do the rest of them mean? What is the difference between ref and ref_count?

vcf-stats vcf

I think a head of the stats file would help portray the differences better.

1 answer

From a few months ago: Vcftools Vcf-Stats Field Definitions

Log in to answer this question.