tag:blogger.com,1999:blog-7785493.post6475551647831614178..comments2024-01-04T04:11:55.717+02:00Comments on Dienekes’ Anthropology Blog: Early Homo mtDNA relic in the human nuclear genomeDienekeshttp://www.blogger.com/profile/02082684850093948970noreply@blogger.comBlogger2125tag:blogger.com,1999:blog-7785493.post-46456440856676202992010-12-11T23:50:19.005+02:002010-12-11T23:50:19.005+02:00I did all my pruning on the HGDP dataset of 940 in...I did all my pruning on the HGDP dataset of 940 individuals, as that has the broadest human coverage. I don't reprune from scratch every time I choose another subset of populations, hence all my (recent) analyses invariably use 177k SNPs. This helps things relatively comparable between them.Dienekeshttps://www.blogger.com/profile/02082684850093948970noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-19097051986496299002010-12-11T22:52:44.653+02:002010-12-11T22:52:44.653+02:00Dienekes, I'm curious as to what populations y...Dienekes, I'm curious as to what populations you used to generate the plink.prune.in file for your standard K=10, 692 samples, 36 population barplot of Eurasian samples. You said with r2 = 0.3 you obtained 177K SNPs. With r2 = 0.3 I got 155K SNPs. But I used all the 692 samples to generate plink.prune.in. When I used just a few populations, I got 176K SNPs.aargiedudehttps://www.blogger.com/profile/02885756901119408472noreply@blogger.com