kiran b2127e59c4 A first draft of scripts and LaTeX templates required to automatically generate slides for the 1,000 Genomes Automated Data Processing Report. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3652 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-28 14:30:50 +00:00
..
1kgScripts	/tmp is failing...	2009-10-08 18:13:49 +00:00
maf_annotation	Passing just the single alternate allele to the converted maf on the recommendation of mike lawrence and kiran.	2010-03-17 19:08:37 +00:00
reports/1KG	A first draft of scripts and LaTeX templates required to automatically generate slides for the 1,000 Genomes Automated Data Processing Report.	2010-06-28 14:30:50 +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	Stupid cent_os doesn't allow old style 'sort' conventions. Updating liftover script...	2010-06-17 13:44:03 +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	A script to sanity check that a release is runnable.	2010-05-26 17:45:42 +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