ebanks 3d988576a6 updated liftover script: it no longer needs to re-sort the vcf ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4501 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-15 08:03:41 +00:00
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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
AnnotateVCFwithMAF.pl	One more fix: exclude input VCF file's directory name from the output file.	2010-09-08 03:09:08 +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
createTranscriptToGenomicInfoTables.pl	Adding a script to do big table conversion. Removing Ben's script which is totally obsolete and busted.	2010-10-12 01:40:43 +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	updated liftover script: it no longer needs to re-sort the vcf	2010-10-15 08:03:41 +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
runPipelineSanityCheck.pl	Added 'Cron' to subject for easier message filtering	2010-09-28 21:03:50 +00:00
runReleaseSanityCheck.pl	- Update DoC to support output to /dev/null.	2010-09-08 23:43:18 +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