ebanks 1c056ea791 Users can now use VariantAnnotator to add annotations from one VCF to another. For example, if you want to annotate your target VCF with the AC field value from the rod bound to CEU1kg, you can specify -E CEU1kg.AC and records will be annotated with CEU1kg.AC=N when a record exists in that rod at the given position. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4598 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-29 16:38:31 +00:00
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annotator	Users can now use VariantAnnotator to add annotations from one VCF to another. For example, if you want to annotate your target VCF with the AC field value from the rod bound to CEU1kg, you can specify -E CEU1kg.AC and records will be annotated with CEU1kg.AC=N when a record exists in that rod at the given position.	2010-10-29 16:38:31 +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	Updated MNP merging to merge VC records if any sample has a haplotype of ALT-ALT, since this could possibly change annotations. Note that, besides the "interesting" case of an ALT-ALT MNP in a pair of HET sites, this could even occur if two records are hom-var (irrespective of using phasing). Note also that this procedure may generate more than one ALT allele.	2010-10-27 01:50:36 +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	Cleanup for multithreading memory leak during integration tests...unregister MXBean at end	2010-10-28 18:37:42 +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	First pass at a VCF validator. Will test more tonight.	2010-10-19 19:55:49 +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