gatk3的最后一个经典版本3.8

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Geraldine Van der Auwera 1cf66addaa Deprecate tools that were outdated or redundant ReadAdaptorTrimmer (unsound and untested) BaseCoverageDistribution (redundant with DiagnoseTargets) CoveredByNSamplesSites (redundant with DiagnoseTargets) FindCoveredIntervals (redundant with DiagnoseTargets) VariantValidationAssessor (has a scary TODO -- REWRITE THIS TO WORK WITH VARIANT CONTEXT comment and zero tests) LiftOverVariants, FilterLiftedVariants and liftOverVCF.pl (in #1106) (use Picard liftover tool) sortByRef.pl (use Picard SortVCF) ListAnnotations (useless) Also deleted the java archive from the private repository (old junk we never use)		2015-11-20 22:49:40 -05:00
licensing	Updated licenses for 2015	2015-08-06 15:23:11 -04:00
protected	Deprecate tools that were outdated or redundant	2015-11-20 22:49:40 -05:00
public	Deprecate tools that were outdated or redundant	2015-11-20 22:49:40 -05:00
settings/helpTemplates	Numerous doc fixes; mostly formatting and clarifications	2015-05-03 00:28:46 +02:00
.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	Added faster built executable, non-packaged jars.	2014-11-05 00:30:46 +08:00
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	Using `SamIndexes.asBaiSeekableStreamOrNull()` to support `.cram.crai`.	2015-09-14 12:20:36 -04:00

README.md

The Genome Analysis Toolkit

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