ebanks 7a291a8ff3 First pass at a VCF validator. Will test more tonight. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4524 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-19 19:55:49 +00:00
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CombineVariantsIntegrationTest.java	CombineVariants now outputs the command line in the VCF header. Added a new hidden argument to VR walkers called --NoByHapMapValidationStatus to turn off the by-hapmap dbsnp rod behavior. Very useful for experimenting with which sets to use as training data.	2010-09-18 16:06:50 +00:00
CombineVariantsUnitTest.java	Starting the clean up of the sting.utils.genotype code which is all either moving to Tribble, moving to sting.utils.vcf, or being removed.	2010-08-10 02:16:05 +00:00
LiftoverVariantsIntegrationTest.java	Hmm. Apparently variants can get lifted over to different chromosomes. Who knew? Reverting changes from a couple of days ago. The only way to do this correctly (without requiring lots of memory) is to turn off on-the-fly indexing for this walker. Integration tests cover this now.	2010-10-17 02:54:12 +00:00
SelectVariantsIntegrationTest.java	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
ValidateVariantsIntegrationTest.java	First pass at a VCF validator. Will test more tonight.	2010-10-19 19:55:49 +00:00