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Old 07-03-2013, 11:59 PM   #1
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Location: China

Join Date: Feb 2009
Posts: 116
Default questions about vcf-stats output

the output of vcf-stats like this:

        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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