depristo cd293f145b 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. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5939 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-03 20:11:31 +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
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	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
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