gatk-3.8

gatk3的最后一个经典版本3.8

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sjia 9b78a789e2 HLA Caller 2.0 Walkers: CalculateBaseLikelihoodsWalker.java walks through reads calculates likelihoods using SSG at each base position CalculateAlleleLikelihoodsWalker.java walks through HLA dictionary and calculates likelihoods for allele pairs given output of CalculateBaseLikelihoodsWalker.java CalculatePhaseLikelihoodsWalker.java walks through reads and calculates likelihoods score for allele pairs given phase information File Readers: BaseLikelihoodsFileReader.java reads text file of likelihoods outputted by SSG FrequencyFileReader.java reads text file of HLA allele frequencies PolymorphicSitesFileReader.java reads text file of polymorphic sites in the HLA dictionary SAMFileReader.java reads a sam file (used to read HLA dictionary when in another walker) SimilarityFileReader.java reads a text file of how similar each read is to the closest HLA allele (used to filter misaligned reads) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1744 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-29 20:45:55 +00:00
R	R script for selecting a variety of baits (using %GC content and normalized coverage) for Nanostring assessment from those used in the Agilent whole exome hybrid selection design.	2009-09-22 18:10:14 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	HLA Caller 2.0 Walkers:	2009-09-29 20:45:55 +00:00
packages	moving IndelGenotyper out from playground	2009-09-25 19:43:53 +00:00
perl	add wait id for 454	2009-09-22 01:41:58 +00:00
python	Detects unmapped (no bai) bam files and doesn't blow up	2009-09-25 12:56:28 +00:00
scala/src	support for scala walkers	2009-08-28 00:15:01 +00:00
settings	Switched to Reflections (http://code.google.com/p/reflections/) project for	2009-07-21 18:32:22 +00:00
shell	Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls AND the compares the geli MD5 sum to the expected one!	2009-09-04 12:39:06 +00:00
testdata	Framework for ROD walkers -- totally experiment and not working right now	2009-09-12 19:13:15 +00:00
build.xml	changes to the variation class, updates to SSG, updated tests based on changes to the SSGenotypeCall, and added the ability to run a single integration test from using the build script.	2009-09-10 04:31:33 +00:00
ivy.xml	Switched to Reflections (http://code.google.com/p/reflections/) project for	2009-07-21 18:32:22 +00:00