ebanks 463bb737c3 Checking in the scripts I'm using for syncing the 1000G mirror. Note that very few people can actually use them because you most likely don't have perission to write to /humgen/1kg/DCC, but these should be used as a resource if anyone ever needs to do this in the future. These scripts are very naive and consist of just the actual pulling down of data. Currently aspera and wget are supported, but Mark should feel free to add lftp if he wants. :) Also, while I'm here, I'm removing obsolete scripts for running an obsolete pipeline. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5282 348d0f76-0448-11de-a6fe-93d51630548a		2011-02-20 03:59:26 +00:00
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maf_annotation	Updated for CentOS changes.	2010-07-08 14:36:24 +00:00
sync1000Genomes	Checking in the scripts I'm using for syncing the 1000G mirror. Note that very few people can actually use them because you most likely don't have perission to write to /humgen/1kg/DCC, but these should be used as a resource if anyone ever needs to do this in the future. These scripts are very naive and consist of just the actual pulling down of data. Currently aspera and wget are supported, but Mark should feel free to add lftp if he wants. :) Also, while I'm here, I'm removing obsolete scripts for running an obsolete pipeline.	2011-02-20 03:59:26 +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