gatk3的最后一个经典版本3.8

chartl 45673d7851 A quick and dirty script that, given a list of input VCF files, will output a new VCF file which looks identical to the first VCF file of the input list, except that the info field has been updated to reflect the union of all the INFO annotations across the VCF files ... Note: this is primarily for use with two files with mostly disjoint annotations. It views "SB=2.5" as a different info field than "SB=2.2" and so will output as info "SB=2.5;SB=2.2". That is, it compares the full field string, rather than only the field name. Usage: ./mergeVCFInfoFields I=[comma-delimited list of files] O=[output file] git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2176 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-29 20:01:29 +00:00
R	R script for selecting a variety of baits (using %GC content and normalized coverage) for Nanostring assessment from those used in the Agilent whole exome hybrid selection design.	2009-09-22 18:10:14 +00:00
c	Add a Unix-standard version number to the file.	2009-11-23 20:07:17 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	Oops. numReads is now called size	2009-11-29 06:59:17 +00:00
packages	Add IlluminaUtil to picard-private.jar	2009-11-25 19:25:21 +00:00
perl	/tmp is failing...	2009-10-08 18:13:49 +00:00
python	A quick and dirty script that, given a list of input VCF files, will output a new VCF file which looks identical to the first VCF file of the input list, except that the info field has been updated to reflect the union of all the INFO annotations across the VCF files	2009-11-29 20:01:29 +00:00
scala/src	Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar.	2009-11-02 06:02:41 +00:00
settings	Push version number of picard-private-parts	2009-11-25 19:28:57 +00:00
shell	Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one!	2009-09-04 12:39:06 +00:00
testdata	GSA-182: Adding support for BED interval files.	2009-10-06 02:45:31 +00:00
build.xml	Build aligner as separate jar file.	2009-11-13 22:29:29 +00:00
ivy.xml	New VariantFiltration.	2009-11-20 19:50:26 +00:00