depristo 1a5d296737 ReplaceReadGroups. Fixes BAM files without read group info. MissingReadGroup points people to this tool now. Please point users on the forum to this tool now. Will migrate to Picard. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5284 348d0f76-0448-11de-a6fe-93d51630548a		2011-02-21 14:02:41 +00:00
..
vcf	and add changes to the vcf used in testing	2010-06-25 02:56:02 +00:00
TabularDataTest.dat	…
TabularDataTest2.dat	…
ValidatingPileupTargets.list	…
defaultGATKConfig.cfg	…
exampleBAM.bam	Fixes for example bam files	2010-10-05 18:43:02 +00:00
exampleBAM.bam.bai	Fixes for example bam files	2010-10-05 18:43:02 +00:00
exampleFASTA.dict	…
exampleFASTA.fasta	…
exampleFASTA.fasta.fai	…
exampleNORG.bam	ReplaceReadGroups. Fixes BAM files without read group info. MissingReadGroup points people to this tool now. Please point users on the forum to this tool now. Will migrate to Picard.	2011-02-21 14:02:41 +00:00
exampleNORG.bam.bai	ReplaceReadGroups. Fixes BAM files without read group info. MissingReadGroup points people to this tool now. Please point users on the forum to this tool now. Will migrate to Picard.	2011-02-21 14:02:41 +00:00
gFFTest.gff	…
logisticParamsTest.list	…
recalConfig_1KG.cfg	…
sampleBedFile.bed	GSA-182: Adding support for BED interval files.	2009-10-06 02:45:31 +00:00
small.dbsnp.rod	a small dbsnp file for Tribble testing	2010-02-18 18:12:55 +00:00
tranches.4.txt	correct test data	2010-11-13 22:17:38 +00:00
tranches.6.txt	VQSR now operates on LOD scores in the INFO field directly, and doesn't adjust the QUAL field. New format for tranches file uses LOD score. Old file format no longer supported. log10sumlog10() function, a very useful utility in MathUtils. No more ExtendedPileupElement! Robust math calculations in GMM so that no infinities are generated! HaplotypeScore refactored to enable use of filtered context. Not yet enabled... InferredContext getDouble and getInteger arguments now parse values from Strings if necessary	2010-11-15 22:19:22 +00:00
tranches.raw.dat	VQSR now operates on LOD scores in the INFO field directly, and doesn't adjust the QUAL field. New format for tranches file uses LOD score. Old file format no longer supported. log10sumlog10() function, a very useful utility in MathUtils. No more ExtendedPileupElement! Robust math calculations in GMM so that no infinities are generated! HaplotypeScore refactored to enable use of filtered context. Not yet enabled... InferredContext getDouble and getInteger arguments now parse values from Strings if necessary	2010-11-15 22:19:22 +00:00