andrewk 369cc50802 Added playground walker that does a basic concordance check between two VCF files - an eval and a truth file - across all samples in the eval file. Produces per-sample, per-locus debug info and simple concordance stats. This is not meant to be extended, but rather used for validating the HapMap to VCF conversion in preparation for retiring GFF-based HapMap data. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2813 348d0f76-0448-11de-a6fe-93d51630548a		2010-02-09 02:41:18 +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	Added playground walker that does a basic concordance check between two VCF files - an eval and a truth file - across all samples in the eval file. Produces per-sample, per-locus debug info and simple concordance stats. This is not meant to be extended, but rather used for validating the HapMap to VCF conversion in preparation for retiring GFF-based HapMap data.	2010-02-09 02:41:18 +00:00
test/org/broadinstitute/sting	VCF->beagle and VCF phasing using beagle input. Appears to work fairly well. VariantContexts now support phased genotypes.	2010-02-09 01:22:05 +00:00