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  • questions about vcf-stats output

    the output of vcf-stats like this:

    Code:
            Rows with a call  3264597
            SNP alleles       2594406
            indel alleles     618033
            other events      0
            ref homs    1107825 (33.9%)
            nonref homs 1055574 (32.3%)
            ref hets    1101105 (33.7%)
            nonref hets 0 (0.0%)
    I don't understand the means of "ref homs, nonref homs, ref hets, nonref hets". According to my understand, for one site, the reference genotype is "A"
    ref homs: A (ref), A (sample)
    nonref homs: A (ref), G (sample)
    ref hets: A (ref), A/T (sample)
    nonref hets: A (ref), T/C (sample)

    Is it right?

    Thank you!

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