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gatk3的最后一个经典版本3.8
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Scala 3.8%
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kiran 6e389059cf An improved version of VariantSubset and VariantSelect, meant to replace those walkers. Takes in a VCF and creates a subsetted VCF by sample(s), JEXL expressions, or both. 
When subsetting by sample, the -SN argument is treated as a literal sample name and, if no match is found, as a regular expression.  This allows for a large number of samples to be selected at once (useful when, for instance, cases are given one sample name prefix and controls are given another).

After the subsetting procedure, the INFO-field annotations AC, AN, AF, and DP are all recalculated to properly reflect the new contents of the VCF.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3968 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-08-08 02:57:06 +00:00
R Publication tranches report is now the default output 2010-08-07 13:58:59 +00:00
archive Archiving 2010-07-27 02:47:18 +00:00
c Reduce file handle usage. 2010-01-05 18:03:01 +00:00
doc moved to wiki 2009-07-22 16:35:23 +00:00
java An improved version of VariantSubset and VariantSelect, meant to replace those walkers. Takes in a VCF and creates a subsetted VCF by sample(s), JEXL expressions, or both. 2010-08-08 02:57:06 +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 Updated resources package descriptor with dbsnp 129 for b37. 2010-08-03 02:42:48 +00:00
perl 1. Updated tests and added integration test for liftover code. 2010-07-12 17:58:18 +00:00
python now support -o output option, useful for pipelines 2010-08-06 14:57:04 +00:00
ruby Adding the ruby directory, and a simple script to restart Bamboo 2009-12-03 22:48:48 +00:00
scala Switch to newer version of comp tracks (and make the trigger track a comp as well). Indel cleaning should override the interval list and only use the contig interval list; and also force jobs to go to long. 2010-08-04 20:05:27 +00:00
settings fix for a bug deep in the tribble indexing: if you had a single record in the first contig, the second contig's index blocks would point to the wrong file seek location, and you'd see no 2010-07-23 18:39:55 +00:00
shell Useful script to see the status of gsa computing resources. Crontab'd and will be arriving as email at 8 am 2010-08-07 12:36:28 +00:00
testdata and add changes to the vcf used in testing 2010-06-25 02:56:02 +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 VariantContext has now moved over to Tribble, and the VCF4 parser is now the only VCF parser in town. Other changes include: 2010-08-05 18:47:53 +00:00
ivy.xml VariantContext has now moved over to Tribble, and the VCF4 parser is now the only VCF parser in town. Other changes include: 2010-08-05 18:47:53 +00:00