Guillermo del Angel 972d6531b6 Corner case fix for indel GL computation: sometimes (depending on surrounding context) reads which are not informative of two candidate haplotypes end up having marginally higher likelihoods with one haplotype as opposed to another, depending on uncertainty on alignments in surrounding regions. So, a sample whose GL is -0.0001,-0.0005,-0.001 may have its genotype set to 1/1 due to this statistical noise. We already have a tolerance comparing max(gl)-min(gl) to avoid genotyping, so this tolerance is now increased from 0.001 to 0.1 (equivalent to 1 PL unit) to avoid genotyping a sample if all PLs are within this threshold. Changed 2 integration test md5s that hit this case.		2012-04-26 10:15:26 -04:00
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R	Add warning message about ratios in variantQCreport, give ratio for MAF > 10%	2012-04-25 12:22:32 -04:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Corner case fix for indel GL computation: sometimes (depending on surrounding context) reads which are not informative of two candidate haplotypes end up having marginally higher likelihoods with one haplotype as opposed to another, depending on uncertainty on alignments in surrounding regions. So, a sample whose GL is -0.0001,-0.0005,-0.001 may have its genotype set to 1/1 due to this statistical noise. We already have a tolerance comparing max(gl)-min(gl) to avoid genotyping, so this tolerance is now increased from 0.001 to 0.1 (equivalent to 1 PL unit) to avoid genotyping a sample if all PLs are within this threshold. Changed 2 integration test md5s that hit this case.	2012-04-26 10:15:26 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller.	2012-04-17 14:22:48 -04:00
testdata	continuing the BQSR triage...	2012-04-05 14:34:15 -04:00