gatk3的最后一个经典版本3.8

Mark DePristo d5d87c50e6 Updates to GeneralCallingPipeline ... -- GCP: use 1% bad variants and 1000 min bad variants -- Don't use project consensus for SNP recal -- Update GCP to assess hapmap and omni sensitivity -- Update the Eval command to use the right hapmap and omni comparisons (per sample) -- Update GCP to use current best filtering parameters -- SNPs: QD, FS, DP, ReadPosRankSum, MQRankSum -- indels: FS, DP, ReadPosRankSum, MQRankSum		2013-04-23 13:55:59 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Bugfix for CommonSuffixSplitter	2013-04-21 19:37:01 -04:00
public	Minor: bump up the amount of cached log10 data in MathUtils so that Monkol can actually call 50K samples.	2013-04-19 08:39:08 -04:00
settings	Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec).	2013-04-05 00:52:32 -04:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Disable Contracts for Java for tests	2013-04-04 11:56:17 -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
ivy.xml	Brought all of ReduceReads to fastutils	2013-02-23 22:53:23 -05:00