gatk3的最后一个经典版本3.8

carneiro 35a4f1e366 .Added VariantEval as an optional step in the pipeline. ... .Lifted to HapMap 3.3 .Lifted to dbSNP 132 where possible. .Added the CEU-Trio WEx(hg19) dataset .Added some options to the pipeline You can now use : -dataset WEX -dataset HiSeq ... to choose which datasets to run through the pipeline. You can now without BAQ and indel mask: -noBAQ -noMASK Choose not to run the gold standard comparison analysis: -skipGoldStandard Activate the VariantEval walker analysis on the Recalibrated vcf: -eval The default behavior is to run exactly like it used to, so this version shouldn't change the way you used to use the pipeline. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5004 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-14 21:55:02 +00:00
R	This updates the script to produce a more tearsheet-like output for sample set statistics. Formatting will be updated for aesthetic improvements. There are also several database options that currently pull out misleading information because of changes in sequencing methodology that will be updated to show correct information. Eventually, plot formatting will be updated as well and additional informative plots will be added.	2011-01-13 15:59:06 +00:00
archive	Eric broke the build. Eric broke the build.	2010-12-15 17:01:38 +00:00
c	Bug fixes for the bwa aligner and changes to support compiling against newer releases of the bwa code base.	2010-12-17 14:49:15 +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	Rewrote warning message to discourage use of unsafe mode.	2011-01-14 21:32:53 +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	Adding the native jna support libraries from the jna.jar to the Queue package jar.	2011-01-08 10:48:30 +00:00
perl	Fixed bug that required users to use the recordOriginalLocation option	2011-01-05 23:12:14 +00:00
python	Deleting old python code	2011-01-07 21:33:45 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	.Added VariantEval as an optional step in the pipeline.	2011-01-14 21:55:02 +00:00
settings	Update Picard / sam-jdk at Tim's request.	2011-01-03 02:17:25 +00:00
shell	watch -n 30 shell/pipelineJobs.csh for those who want to watch the gsaadm's jobs progress	2011-01-09 13:09:30 +00:00
testdata	VQSR now operates on LOD scores in the INFO field directly, and doesn't adjust the QUAL field. New format for tranches file uses LOD score. Old file format no longer supported. log10sumlog10() function, a very useful utility in MathUtils. No more ExtendedPileupElement! Robust math calculations in GMM so that no infinities are generated! HaplotypeScore refactored to enable use of filtered context. Not yet enabled... InferredContext getDouble and getInteger arguments now parse values from Strings if necessary	2010-11-15 22:19:22 +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	FASTQ directory is gone	2011-01-13 15:16:06 +00:00
ivy.xml	Removed stochasticity from IndelRealigner by random sampling using and seed based on the read list.	2011-01-07 22:03:36 +00:00