ebanks e50627a49e 1. Updated tests and added integration test for liftover code. ... 2. Updated liftover code (and scripts) to emit vcf 4.0 and no longer depend on VCFRecord. 3. Beagle walker now also emits vcf 4.0. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3767 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-12 17:58:18 +00:00
..
1kgScripts	/tmp is failing...	2009-10-08 18:13:49 +00:00
maf_annotation	Updated for CentOS changes.	2010-07-08 14:36:24 +00:00
reports/1KG	Updates to not depend on an environment variable to figure out where libraries are (helpful for installation at the Sanger).	2010-06-28 15:46:41 +00:00
DataTable.pm	A quick module to load up text files more easily	2010-03-12 02:31:29 +00:00
DistributedMake.pm	Some useful changes that I've had laying around for a while - deletes files from failed runs, automatically adds a memory limit to java commands where one isn't specified, and touches files on the local machine after command completion to get around the problem with the times not being perfectly synchronized across LSF nodes.	2010-02-12 00:18:34 +00:00
StingArgs.pm	A useful perl module for quick argument parsing.	2009-08-31 15:44:57 +00:00
batchGATKjobsWithRegExp.pl	perl script to make batching jobs easier	2009-09-16 19:02:46 +00:00
enqueueGATKcallerJobs.pl	Some useful scripts for running only individual parts of the pilot1/2 cleaning/calling pipeline	2009-09-11 17:38:33 +00:00
filterSingleSampleCalls.pl	Adding the post-processing indel filter to GATK	2010-04-27 14:43:39 +00:00
liftOverVCF.pl	1. Updated tests and added integration test for liftover code.	2010-07-12 17:58:18 +00:00
randomSampleFromStream.pl	A little gadget to select random samples from input stream(s) of unknown length. By default, selects a single line (with probability 1/TOTAL_NUMBER_OF_LINES_READ), with -N option randomly selects specified number of lines. Can read from STDIN or from arbitrary number of input streams (all streams will be merged). Examples:\n cat file1 file2 file3 | randomSampleFromStream.pl -N 5 \n\n or \n randomSampleFromStream.pl file1 file2 file3	2009-07-31 18:55:14 +00:00
runReleaseSanityCheck.pl	fixed typos	2010-07-07 17:41:44 +00:00
sortByRef.pl	bug fix: now contigs not present in the sequence dictionary are registered properly and do not cause the script to break	2010-06-23 20:59:38 +00:00
splitAndEnqueueGATKjobs.pl	rename some jobnames so that LSF doesn't complain	2009-09-18 19:02:15 +00:00