chartl 2bc5971ca1 Added - a tool to fix reference bases of a VCF. The OMNI had a couple of sites with incorrect reference bases (look to be legacy from other chips), and a few more that had ref and alt flipped. GAP should probably take care of it, but since I need results by monday, I'm doing it. ... Modified - SelectVariants: Hook up to VariantContextUtils to recalculate AC/AF/AN, which uses the accessor in VariantContext to do this. Somehow sites that were selected down to hom-ref genotypes only wound up getting positive AC. **IMPORTANT** I kind of need input here. The header of a file used for an integration test specifies AC as being an integer. Recalculating it casts it into an integer list (which it should be, as it allows for alternate alleles). However this appears to clash with what the jexl expression is looking for? For now, the integration test itself needed to be changed -- it's unclear what to do when the header specifies AC of being one class, but recalculating it casts to another class, and I'm not sure what to do. I'm committing my omni_qc pipeline because I'm almost certain 2 months down the road I'm going to wonder what the heck I did to generate my results. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4511 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-17 03:18:01 +00:00
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annotator	updating integration test for Sarah Calvo	2010-10-07 04:03:37 +00:00
beagle	Somewhat major update. Changes:	2010-10-08 13:30:28 +00:00
coverage	Small change for Matt -- output partition types in lexicographic order.	2010-09-28 20:08:03 +00:00
fasta	I just spoke to Andrey & Kiran (the original authors of these tools), and they voted to kill these in favor of Picard	2010-09-20 13:27:35 +00:00
filters	Three fixes for VariantFiltrationWalker: Trying to filter an empty VCF file will produce a well-formed VCF file with zero records instead of a blank file, needed for pipelines. The first record's genotype info fields are now in the same order as all the others. The VCF header lines are pulled from just the input variant rod instead of from all rods.	2010-09-24 13:52:56 +00:00
genotyper	More test cases for UG integration test. We currently fail doing multi-threaded gzip output, FYI	2010-10-08 20:22:12 +00:00
indels	Hack to fix mysterious disappearing read attributes. Ultimately caused	2010-10-13 19:06:54 +00:00
phasing	Changed min MQ and BQ to 20 (for phasing)	2010-10-08 19:27:45 +00:00
qc	GATK now detects and UserExceptions when human lexicographically sorted data is provided	2010-09-24 15:19:48 +00:00
recalibration	CombineVariants now outputs the command line in the VCF header. Added a new hidden argument to VR walkers called --NoByHapMapValidationStatus to turn off the by-hapmap dbsnp rod behavior. Very useful for experimenting with which sets to use as training data.	2010-09-18 16:06:50 +00:00
sequenom	Removed the SequenomValidationConvertor and renamed it VariantValidationAssessor since it no longer handles ped/sequenom files (but instead works on vcfs/variantcontexts). Updated all of the wiki docs, including adding instructions on how to convert ped files to vcf, a la Shaun Purcell. We now officially no longer support ped files everyone. Other misc cleanup in the code.	2010-10-04 02:11:38 +00:00
varianteval	This is simultaneously a minor and major change to VariantEval, so take heed:	2010-10-13 22:26:15 +00:00
variantrecalibration	2nd step towards on the fly indexing. Also fixed parsing bug for headers with < symbols	2010-10-07 21:38:46 +00:00
variantutils	Added - a tool to fix reference bases of a VCF. The OMNI had a couple of sites with incorrect reference bases (look to be legacy from other chips), and a few more that had ref and alt flipped. GAP should probably take care of it, but since I need results by monday, I'm doing it.	2010-10-17 03:18:01 +00:00
ClipReadsWalkersIntegrationTest.java	The battle is over. Picard is revved.	2010-09-03 05:28:01 +00:00
PileupWalkerIntegrationTest.java	removal of most of the old GATK ROD system; also a fix for -Dsingle so we can again run just a single unit or integration test (single tests in tribble can be run with the -DsingleTest option now). More to come.	2010-09-15 22:54:49 +00:00
PrintReadsWalkerUnitTest.java	Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.	2010-08-22 14:27:05 +00:00
VariantsToVCFIntegrationTest.java	The engine now automatically adds the command-line arguments to the header of every VCF, unless -NO_HEADER is specified.	2010-09-22 15:27:58 +00:00