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
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/.
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.
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Nothing? I guess I'll email Dr. Altshuler, the corresponding author for the international Hapmap.
How do you know all the SNPs that fails HWE has been removed? Is there an official doc somewhere? -Thanks