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	Revised ROD system. Split the system in Basic type and interface. Enabled more control over rod accessing, including an initialize() function to fetch headers and other options from the file. Added general tabular rod, which has a named columns and supports a map<String,String> interface. Comes with shiny new Junit system for RODs. Also, added simple python script for accessing picard data.	2009-05-14 21:06:28 +00:00
TabularDataTest2.dat	Better interface to the tabular ROD, now makes writing files easier. Also has corresponding test files	2009-05-14 23:20:11 +00:00
ValidatingPileupTargets.list	Framework for ROD walkers -- totally experiment and not working right now	2009-09-12 19:13:15 +00:00
defaultGATKConfig.cfg	Apprach v2. Added python analysis script, so java no longer must be used to analyses quality score data. About to refactor out lots of unneeded code	2009-06-20 16:00:23 +00:00
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	Derive examples from real data.	2009-07-10 04:21:37 +00:00
exampleFASTA.fasta	Derive examples from real data.	2009-07-10 04:21:37 +00:00
exampleFASTA.fasta.fai	Derive examples from real data.	2009-07-10 04:21:37 +00:00
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	Skeleton of new directory structure.	2009-03-11 20:05:05 +00:00
logisticParamsTest.list	Basic logistic regression support for calibrating qualities; mostly for Andrew to experiment with	2009-04-24 19:09:50 +00:00
recalConfig_1KG.cfg	I've pulled out the functionality of the analyzer into a single python file which doesn't require all of the irrelevant config parameters (which would cause problems for external users). I'll release this and the simple config file to 1KG for use in analyzing recalibration efforts.	2009-08-11 02:56:43 +00:00
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