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1kgScripts
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update script to put pilot1 bams directly onto hphome
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2009-09-08 14:41:35 +00:00 |
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genomicAnnotatorScripts
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Added handling of UCSC and NCBI reference sequences
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2010-04-14 14:40:31 +00:00 |
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AlignBam.py
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Give usage message if no arguments provided.
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2009-08-31 00:28:43 +00:00 |
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AlignBams.py
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Short python script that takes paired-end BAMs and aligns them with BWA. Referenced in GSA wiki tutorial
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2009-07-31 00:04:10 +00:00 |
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AnnotateVCFwithMAF.py
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Make annotated VCF not be broken
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2010-03-01 23:22:41 +00:00 |
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BarcodeAnalysis.py
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Added command line options to make the barcode analysis script executable by end users.
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2009-08-24 21:15:09 +00:00 |
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CoverageEval.py
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Updated SNP calling power from coverage tools to work with new UnifiedGenotyper and DepthOfCoverage tools.
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2009-12-16 20:44:30 +00:00 |
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CoverageMeta.py
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Updated SNP calling power from coverage tools to work with new UnifiedGenotyper and DepthOfCoverage tools.
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2009-12-16 20:44:30 +00:00 |
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DOCParameter.py
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Checking in Michael's DoC parameterization script;
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2009-09-03 15:07:49 +00:00 |
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EvalMapping.py
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FastaQuals2Fastq.py
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FlatFileTable.py
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Add ability for flat file table parsing module to skip ahead to first occurence of a regular expression (use case: consistently parsing DepthOfCoverage output for histogram section of file across file format changes)
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2009-12-16 20:38:50 +00:00 |
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Geli2GFF.py
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Gelis2PopSNPs.py
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Fixing odd merge problem with VariantEval -- better cluster analysis (no cumsum), rodVariant is now an AllelicVariant
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2009-07-14 18:53:27 +00:00 |
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JobDispatcher.py
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Awesome: JobDispatcher can now dispatch jobs by gene from a target .design file found in /seq/references.
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2010-04-14 18:17:41 +00:00 |
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JobDispatcherExample.py
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This is a python job dispatcher I've been using, which builds on Mark's FarmJob utility, and an example script of how I'm using it. Basically I wrote it to smartly break up analysis over an interval list, givin a maximum number of bases per job, a list of available queues, and a limit on each queue. It handles going over these limits in three ways:
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2010-03-31 19:53:13 +00:00 |
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LogRegression.py
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LogisticRegressionByReadGroup.py
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Revert some debug code in RecalQual.py. Make LogisticRegression easier to Ctrl-C out of.
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2009-06-05 01:53:48 +00:00 |
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MergeBAMBatch.py
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Fixes for VariantEval for genotyping mode
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2009-09-18 21:01:43 +00:00 |
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MergeBAMsUtils.py
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Fixes for VariantEval for genotyping mode
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2009-09-18 21:01:43 +00:00 |
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MergeBamsByKey.py
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Trivial change
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2009-06-12 19:11:28 +00:00 |
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MergeEvalMapTabs.py
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ParseDCCSequenceData.py
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Added ParseDCCSequenceData.py to repository and made changes that allow an analysis of quantity of sequence data by platform and project, moved table / record system to a new module called FlatFileTable.py and built that into ParseDCCSequenceData and CoverageEval.py; changed lod threshold in CoverageEvalWalker.
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2009-07-08 22:04:26 +00:00 |
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RecalQual.py
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Updated version of the recalibration tool
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2009-06-19 17:45:47 +00:00 |
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RefseqLibrary.py
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Awesome: JobDispatcher can now dispatch jobs by gene from a target .design file found in /seq/references.
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2010-04-14 18:17:41 +00:00 |
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RunPilot2Pipeline.py
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Fix merger command
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2009-09-11 13:13:23 +00:00 |
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SAM.py
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SamWalk.py
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SamWalkTest.py
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SimpleSAM.py
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SimulateReads.py
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SpawnMapperJobs.py
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SpawnValidationJobs.py
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StressTestGATK.py
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SyzygyCallsFileToVCF.py
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Minor changes (additional info calculated)
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2010-01-06 16:41:01 +00:00 |
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VCFValidationAnalysis.py
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A collection of python objects that are useful for VCF validation. Use 'em or don't.
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2010-01-25 18:44:10 +00:00 |
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ValidateGATK.py
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Actually listens to justPrint now
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2009-07-15 16:52:46 +00:00 |
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Verify1KGArchiveBAMs.py
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interim update
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2010-04-15 14:25:02 +00:00 |
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WalkLociTest.py
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Walker.py
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aln_file.nocvs.py
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aln_file.py
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callingProgress.py
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simple monitor for watching pilot 1 call progress
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2009-10-06 13:04:53 +00:00 |
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collectCalls.py
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Adding this to subversion so it's protected
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2009-12-09 21:26:17 +00:00 |
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compSNPCalls.py
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countCoverageWithSamtools.py
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create_venn_evals.py
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Script to split concordance files into their constituent sets and calculate summary stats from a concordance file - SNPs called and number in dbSNP
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2010-03-12 22:20:44 +00:00 |
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easyRecalQuals.py
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Updated python files
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2009-07-07 14:15:39 +00:00 |
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expandedSummaryToVCF.py
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Oops. Let's make sure only to write calls that the pool supports to the auxiliary vcf files.
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2009-11-04 17:14:55 +00:00 |
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faiReader.py
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Better snpSelector, plus VCFmerge tool
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2009-11-11 22:02:57 +00:00 |
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farm_commands.py
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Now supports strings in command line for farm submission
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2010-01-06 13:15:40 +00:00 |
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farm_commands2.py
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better farm commands, and simple utility to convert ucsc repeat masks to interval lists
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2010-03-19 13:11:06 +00:00 |
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fasta.py
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gatkConfigParser.py
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High performance LocusIterator implementation. Now with greatly reduced memory impact and 2x (and more potentially) speed ups of raw locus iteration. General performance improvements to SSG with empirical probs. You can enable high-performance locus iteration with the -LIBS arg. It's still testing but passes validing pileup.
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2009-09-03 03:06:25 +00:00 |
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generate1KGHapmapVCF.py
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Quick script that changes "chr#" to "#" and "chrM" to "MT" and moves mitochondria to the end of the vcf; in accordance with the 1KG reference.
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2010-01-28 21:59:33 +00:00 |
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getBamFilesFromSpreadsheet.py
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Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics
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2010-03-29 13:32:00 +00:00 |
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getTargetedGenes.py
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Just some code I want to freeze. If you ever need to estimate the % of bases covered by exon, given an interval list, give it to getTargetedGenes. Not the best name for this function, but I don't expect anyone to use it but me.
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2010-04-01 20:21:50 +00:00 |
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makeMetricsFilesForFirehose.py
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Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics
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2010-03-29 13:32:00 +00:00 |
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memo.py
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mergeVCFInfoFields.py
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Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics
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2010-03-29 13:32:00 +00:00 |
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mergeVCFs.py
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new -a option does fast merging of already sorted files
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2010-01-05 13:55:39 +00:00 |
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picard_utils.py
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Updated python files
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2009-07-07 14:15:39 +00:00 |
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pilot2CallingPipeline.py
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keeping a backup
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2010-01-31 15:36:25 +00:00 |
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pushback_file.py
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qltout.py
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samtooltest.sh
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snpSelector.py
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snpSelector now supports min and max q scores.
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2010-01-31 19:38:34 +00:00 |
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tgtc2sam.py
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ucscRepeatMaskToIntervalList.py
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better farm commands, and simple utility to convert ucsc repeat masks to interval lists
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2010-03-19 13:11:06 +00:00 |
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vcf2table.py
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updates to the python snp selector -- now sorts info fields and we stop printing unnecessary debugging info in vcf2table
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2009-12-04 22:16:02 +00:00 |
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vcfReader.py
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minor improvements to snpSelector to work with hapmap chip VCF files
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2009-12-13 17:59:32 +00:00 |
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