chartl 21ec44339d Somewhat major update. Changes: ... - ProduceBeagleInputWalker + Now takes a validation ROD and a prior to give it, will use those genotypes in place of the variant genotypes if both are present + Takes a bootstrap argument -- can use some given %age of the validation sites + Optionally takes a bootstrap output argument -- re-prints the validation VCF, filtering those sites used as part of the bootstrap -BeagleOutputToVCFWalker + Now filters sites where the genotypes have been reverted to hom ref + Now calls in to the new VCUtils to calculate AC/AN -Queue + New pipeline libraries for easy qscript creation, still a work in progress, but this is a considerable prototype + full calling pipeline v2 uses the above libraries + minor changes to some of my own scripts + no more need for contig interval lists, these will be parsed out of your normal interval list when it is provided git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4459 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-08 13:30:28 +00:00
..
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	Officially fixed the UG priors; updated the default min MQ/BQs to pipeline values of q20 and min calling threshold to Q50	2010-10-05 18:35:36 +00:00
indels	Damnit. Enabling the Picard code to recalculate all of the relevant SAMRecord attribute tags means that I need to have reference bases over all read bases even after realignment (and there are some big indels in dbsnp). Fortunately, I have my trusty IndexedFastaSequenceFile reader handy! Re-enabling the previously broken performance test.	2010-09-12 05:06:37 +00:00
phasing	1. Phasing now ignores bases without minimum base quality (BQ) and minimum mapping quality (MQ); 2. The probability of a non-called base is now divided by 3, to evenly split up the error probability over the non-called bases	2010-10-07 17:40:59 +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	Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax	2010-08-25 03:47:57 +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	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
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