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brentp / peddy

genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF

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How many Snps used in the PCA ?

ymavura3 opened this issue · comments

commented

Hi Brent, I am using Peddy to get ancestry from VCF files from RNA-seq samples which have 5-15 million uniquely mapped reads, so the quality is not great. My question is, how do I know how many snps were used in the PCA ? This is quite important in my analysis.
Thanks.
Yusuph.

commented

you can look at het_check.csv and look at the sampled_sites column to know how many sites were used in the PCA.