depristo 4c6d0e6143 Added stratification by discrete allele count, just like AF, but requiring genotypes so it can be exact. Added docs on wiki, and integrationtest using Kiran's very nice fundamental VCF ... VariantEvalWalker now passes a pointer to itself to the Stratefication setVariantEvalWalker (and assoc. get method) so that stratefications can look at VEWalker variables to obtain information necessary for their calculations, like the list of eval samples. This is a better interface, in my opinion, than the current approach of extending the base abstract Stratefication to include an initialize function that has all arguments necessarily for any Strat. JEXL expressions now provide access to the VariantContext vc object itself, so you can write JEXL's that directly use VariantContext and associated functions from the command line. ExomePostQC Queue script now creates a byAC eval using the new strat, and no longer produces a byAF file (as this was not exact, and lead to strange punctile behavior when actual AF quantization was out of sync with fix quantization of AF strat. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6015 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-19 03:11:00 +00:00
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1kg_table1.scala	Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output.	2011-03-24 14:03:51 +00:00
AssessChipCoverageOfPanel.q	Computes how well a genotype chip covers a reference panel	2011-05-14 15:07:28 +00:00
CleaningTest.scala	Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output.	2011-03-24 14:03:51 +00:00
ExomePostQCEval.scala	Added stratification by discrete allele count, just like AF, but requiring genotypes so it can be exact. Added docs on wiki, and integrationtest using Kiran's very nice fundamental VCF	2011-06-19 03:11:00 +00:00
IndelCallerEvaluation.scala	Simple program that calls indels in CEU trio exomes and WGS can compared the results. Overall the indel calls really look good to me, given reasonably good input BAM files.	2011-06-16 12:56:04 +00:00
PrepareBamsForHomogeneityTesting.scala	More stable reduced reads representation. Bug fixes throughout. No diffs by <1% of sites in an exome, and the majority of these differences are filtered out, or are obvious artifacts. UnitTests for BaseCounts. BaseCounts extended to handle indels, but not yet enabled in the consensus reads.	2011-06-03 20:11:31 +00:00
ReducedBAMEvaluation.scala	Significant performance optimization for reduced reads due to better algorithm for including reads in the variable regions. Fixed a critical bug that actually produced multiple copies of the same read in the variable regions with this optimization as well. Scala exploration script updated as well.	2011-06-16 12:54:59 +00:00
RefineGenotypesWithBeagle.q	A script for playing with BEAGLE refinement parameters. Supports construction of reference panels from NGS data sets with varying niteration and calibration curve parameters, as well as imputing missing genotypes in a VCF with this reference panel, and comparison to a deeply sequenced individual.	2011-03-27 12:44:25 +00:00
VQSRCutByNRS.scala	Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output.	2011-03-24 14:03:51 +00:00
manySampleUGPerformance.scala	removing dependance on jobQueue == gsa	2011-05-27 10:12:09 +00:00
resequencingSamples1KG.scala	Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output.	2011-03-24 14:03:51 +00:00