gatk-3.8

gatk3的最后一个经典版本3.8

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depristo fc39377e6c Simple pre-processing script for soapsnp files git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4627 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-04 20:34:43 +00:00
R	Takes a list of BAMs, looks up the read group information in the sequencing platform's SQUID database, and computes the tearsheet stats. Also takes the VariantEval output (R format) and outputs the variant stats and some plots for the tearsheet. This script requires the gsalib library to be in the R library path (add the line '.libPaths('/path/to/Sting/R/')' to your ~/.Rprofile).	2010-10-27 19:06:22 +00:00
archive	Fisher exact makes a return. Seems to be working properly. Current tagged as a work in progress. Needs to take the filtered context to be truly correct.	2010-10-22 20:35:53 +00:00
c	Reduce file handle usage.	2010-01-05 18:03:01 +00:00
doc	removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also	2010-08-19 00:42:37 +00:00
java	Unfortunately when annotating sites with the UG the -G None option was wiping out the single annotations added by -A options	2010-11-04 19:27:23 +00:00
matlab	Another matlab script -- this time for making power and coverage plots over a specific gene region. Lots of fun file reading, string manipulation, and exploration of the set() function	2009-11-30 20:02:25 +00:00
packages	Include all standard annotations	2010-10-11 20:52:08 +00:00
perl	Also removed contig intervals from the pipeline sanity check perl scsript.	2010-10-21 11:23:34 +00:00
python	Simple pre-processing script for soapsnp files	2010-11-04 20:34:43 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	My analysis script for private mutations. I'm committing it because it contains a number of specialized command line functions that could prove useful in the future. (For example: ConcatVCF and ExtractSample)	2010-11-04 19:57:27 +00:00
settings	Added status email support with -statusTo. Will send emails on failure of an individual function or success/failure of the whole pipeline.	2010-10-14 15:58:52 +00:00
shell	Inprocess functions by default now log what output files they are running for.	2010-10-07 19:08:02 +00:00
testdata	Fixes for example bam files	2010-10-05 18:43:02 +00:00
LICENSE	Adding a license to the root directory in case BOSC checks for one. Has the	2010-04-20 16:04:29 +00:00
build.xml	Adding packaging system support for external directories.	2010-11-02 20:13:13 +00:00
ivy.xml	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00