gatk3的最后一个经典版本3.8

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Laura Gauthier 9f3cbb2ef1 Improvements to CalculateGenotypePosteriors and CalibrateGenotypeLikelihoods CalculateGenotypePosteriors now only computes posterior probs for SNP sites with SNP priors (other sites have flat priors applied) CalibrateGenotypeLikelihoods had originally applied HOM_REF/HET/HOM_VAR frequencies in callset as priors before empirical quality analysis. Now has option (-noPriors) to not apply/apply flat priors. Also takes in new external probabilities files, such as those generated by CGP, from which the genotype posterior probability qualities will be read. Integration test was changed to account for new SNP-only behavior and default behavior to not use missing priors. (Also, new numRefIfMissing is 0, which should only matter in cases using few samples when you probably don't want to be doing that anyway!)		2014-04-24 08:49:42 -04:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	Improvements to CalculateGenotypePosteriors and CalibrateGenotypeLikelihoods	2014-04-24 08:49:42 -04:00
public	Allow for non-tab whitespace in sample names when performing on-the-fly sample-renaming.	2014-04-22 11:07:13 -04:00
settings/helpTemplates	Replaced local drmaa and Jama artifacts with versions from maven central.	2014-02-22 01:21:35 +08:00
.gitignore	Fixed bug using GraphBased due to infinite likelihoods resulting from the calculation of alignment cost of very long insertion or deletions (done in linear scale)	2014-04-01 16:14:52 -04:00
README.md	Update README file for the 2.6 release	2013-06-20 13:08:29 -04:00
ant-bridge.sh	Rename existing PipelineTests to QueueTests to prepare for upcoming push of new pipeline tests	2014-03-10 21:24:03 -04:00
intellij_example.tar.bz2	Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!)	2012-09-27 11:04:56 -04:00
pom.xml	Quoting -out parameter during resource bundle (StingText.properties) creation.	2014-04-15 17:06:49 +08:00

README.md

The Genome Analysis Toolkit

See http://www.broadinstitute.org/gatk/