Downloading Snps Which Failed Hardy-Weinberg From Hapmap Or 1000G Data

Question

[Ryan D]

Looking at the current releases of Hapmap, it seems SNPs which failed Hardy-Weinberg have been removed. I guess this is probably so people can impute with quality datasets. Whatever the motivation, I want to download specifically SNPs which failed Hardy-Weinberg checks. Is there a version of Hapmap from which to do this or a Hapmart-style interface where one can select SNPs using such criteria?

Thanks, Rx

[Ryan D]

Nothing? I guess I'll email Dr. Altshuler, the corresponding author for the international Hapmap.

[sinorenjianyi]

How do you know all the SNPs that fails HWE has been removed? Is there an official doc somewhere? -Thanks

Answer 1

[Ryan D]

According to David Altshuler, it looks like there is a release for which genotypes for failed SNPs are available. Hapmap SNPs which had genotyping problems or failed HWE tests can be downloaded from here: http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/2007-01/fwd_strand/redundant-unfiltered/.

[Larry_Parnell]

Great question +1 and good to know where those "tossed out" SNPs'genotypes are. I feel there could be a few golden nuggets in this pile of SNPs.