carneiro fa7284b7a1 Genotype And Validate walker is now ready to be used by anyone. ... given an annotated VCF and a BAM file, it genotypes (using the reads in the BAM) each variant in the VCF (for snp or indel) and validates (or not) the 'known' annotation. Outputs a truth table with the PPV and NPV values, and optionally a vcf file with the variants that had enough coverage to be validated. You can optionally provide a minimum depth of coverage and only do the analysis conditional on that. (will write a wiki for this walker, as it might be useful for future validation essays). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5409 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-08 22:10:38 +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	Genotype And Validate walker is now ready to be used by anyone.	2011-03-08 22:10:38 +00:00
test	Added several integration tests for UG indel caller:	2011-03-08 16:21:21 +00:00