gatk3的最后一个经典版本3.8

Mark DePristo 559a4bc05d Updating general calling pipeline to work with newer HC and UG arguments and filtering ... -- Use default VQSR params of QD, FS, DP and MQ for SNPs, with ReadPosRankSum and HaplotypeScore for UG SNPs -- Add combine variants to GeneralCallingPipelin -- Fix incorrect intervals in HaplotypeCaller in GeneralCallingPipeline.scala -- GCP now emits tables for VCFs by default -- GCP runs HC first before UG -- GeneralCallingPipeline now jointly calls input BAMs, not separately processes them. Ready to handle CEU trio calling -- Assess NA12878 on the particularly well reviewed 10-11mb in addition to all of 20 -- Use 4G for HC		2013-03-20 22:54:35 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Merge pull request #120 from broadinstitute/aw_reduce_reads_clear_name_cache	2013-03-20 19:47:42 -07:00
public	Created new DeprecatedToolChecks class	2013-03-20 06:46:02 -04:00
settings	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Fix tests that were consistently or intermittently failing when run in parallel on the farm	2013-03-06 13:56:54 -05:00
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