chartl 1b9184a1c7 Added a multisample concordance walker which takes the place of the VCF python library I've been using. Takes a truth VCF and a variant VCF and outputs A TSV that looks like this: ... Sample_ID Concordant_Refs Concordant_Vars Homs_called_het Het_called_homs False_Positives False_Negatives_Due_To_Ref_Call False_Negatives_Due_To_No_Call NA19381 491 294 2 0 0 0 1 NA19451 489 298 1 0 0 0 0 NA19463 486 289 2 3 1 4 3 NA19376 488 296 1 0 2 0 1 NA19317 489 284 5 3 3 3 1 This walker will be merged with GenotypeConcordance once it's clear how to do so. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2715 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-27 22:59:17 +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 a multisample concordance walker which takes the place of the VCF python library I've been using. Takes a truth VCF and a variant VCF and outputs A TSV that looks like this:	2010-01-27 22:59:17 +00:00
test/org/broadinstitute/sting	Incremental update 2 -- refined allele and VariantContext classes; support for AttributedObject class; extensive testing for Allele class, and partial for VariantContext. Now possible to easily convert dbSNP to VariantContext.	2010-01-27 17:19:37 +00:00