gatk3的最后一个经典版本3.8

Guillermo del Angel 95637e03a0 Updates to pool caller scala script due to new paths and cleanup, hopefully with final changes for paper. ... Added also R script used to process everything into a couple of ggplot-friendly data frames. Functionality is basically the same. Enhancements: -- Add annotation to log axiom and Exome Chip AC along with LOF results for concordance comparisons. -- General Cleanup. -- Used base path for files as a variable in case directory structure in gsa-hpprojects changes again. -- Output also per-pool data by subsetting genotypes per pool and comparing with corresponding genotypes from Axiom, exome chip and omni. -- Commit R scripts that load all tables and crunch them to analyze them.		2013-04-30 10:05:35 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Fix for indel calling with UG in presence of reduced reads: When a read is long enough so that there's no reference context available, the reads gets clipped so that it falls again within the reference context range. However, the clipping is incorrect, as it makes the read end precisely at the end of the reference context coordinates. This might lead to a case where a read might span beyond the haplotype if one of the candidate haplotypes is shorter than the reference context (As in the case e.g. with deletions). In this case, the HMM will not work properly and the likelihood will be bad, since "insertions" at end of reads when haplotype is done will be penalized and likelihood will be much lower than it should.	2013-04-29 19:33:02 -04:00
public	Change Long to long	2013-04-30 09:21:10 -04:00
settings	Rev picard, sam-jdk, tribble, and variant jars to version 1.90.1442	2013-04-25 14:05:24 -04:00
.gitignore	Detect stuck lock-acquisition calls, and disable file locking for tests	2013-04-24 22:49:02 -04:00
build.xml	Add additional necessary class files to na12878kb.jar target	2013-04-23 14:03:48 -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