chartl 341e93ee12 The reference fixer seems to have munged the OMNI rather than making it better. Looks like some sites need to only have the ref and alt bases swapped, and others need to have the genotypes swapped as well? E.g. ... some subset need A C 1/1 --> C A 0/0 while another subset need A C 1/1 --> C A 1/1 it's unclear how big these subsets are (or even if one is empty). What I do know is, doing the first one totally screws up concordance metrics for the 421-sample chip. So either something else needs to be done, or there's a bug in this walker. Until I know for sure, I've added an initialize exception to disable this thing... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4523 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-19 12:50:24 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	The reference fixer seems to have munged the OMNI rather than making it better. Looks like some sites need to only have the ref and alt bases swapped, and others need to have the genotypes swapped as well? E.g.	2010-10-19 12:50:24 +00:00
test	Added - a tool to fix reference bases of a VCF. The OMNI had a couple of sites with incorrect reference bases (look to be legacy from other chips), and a few more that had ref and alt flipped. GAP should probably take care of it, but since I need results by monday, I'm doing it.	2010-10-17 03:18:01 +00:00