fromer 48772a9d01 Fixed bug that required users to use the recordOriginalLocation option ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4944 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-05 23:12:14 +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
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	Had these changes regarding memory cutoffs for a while. Committing them so I can be running a clean codebase, but people shouldn't use this. Queue is way better.	2010-11-27 23:31:31 +00:00
MergeAndEvaluateVCFs.pl	A helper script to merge two VCFs, run VariantEval, and the VariantReport.R script.	2010-11-28 00:45:21 +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	Patch for James	2010-10-20 02:39:16 +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	regexp fixed, now can find OBS_COUNTS followed by both [C/A/R] (obsolete) and [C/A/T] (current)	2010-11-15 15:28:38 +00:00
liftOverVCF.pl	Fixed bug that required users to use the recordOriginalLocation option	2011-01-05 23:12:14 +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	Also removed contig intervals from the pipeline sanity check perl scsript.	2010-10-21 11:23:34 +00:00
runReleaseSanityCheck.pl	Package all walkers in org/broadinstitute/sting/gatk/walkers directory in release.	2010-11-18 02:33:45 +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
tablesorter.pl	Script based on the second part of Eric's createTranscriptToGenomicInfoTables.pl script which sorts flat files by reference order	2010-11-15 19:44:32 +00:00