depristo 27d4b317fc 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. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6006 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-16 12:56:04 +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	Now accepts any number of VCFs to evaluate. Runs the standard (now three) variant eval commands and invokes the exomeQC R script. Has some annoying assumptions about paths encoded right now. Example usage below:	2011-06-16 12:49:54 +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