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brentp / somalier

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

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n in relatedness result

wac opened this issue · comments

commented

Hello! Just wanted to confirm the "n" in the relatedness result (the "pairs.tsv" output file) - I'm guessing that it is perhaps the number of sites shared between sample_a and sample_b?

I'm also guessing the x_ibs0 and x_ibs2 are the expected ibs0 and ibs2 based on the provided pedigree?

Thank you!

commented

Hi, n is the number of sites where both samples have a known genotype.

x_ibs0 and x_ibs2 are like ibs0 and ibs2, but for the x-chromosome only.