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1kgScripts
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genomicAnnotatorScripts
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Fixed error message
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2010-06-28 14:50:28 +00:00 |
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1kgStatsForCalls.py
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misc. useful updates to python library
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2010-06-30 16:33:32 +00:00 |
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AlignBam.py
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AlignBams.py
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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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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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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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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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MergeBAMBatch.py
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MergeBAMsUtils.py
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MergeBamsByKey.py
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MergeEvalMapTabs.py
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ParseDCCSequenceData.py
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RecalQual.py
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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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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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Verify1KGArchiveBAMs.py
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Marginally more useful output
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2010-04-20 14:45:14 +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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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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expandedSummaryToVCF.py
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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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more powerful management routines for my pipeline
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2010-05-12 13:37:39 +00:00 |
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fasta.py
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gatherIndelsToVCF.py
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Added - Q&D script to gather verbose bed files to a VCF.
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2010-05-05 02:49:16 +00:00 |
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gatkConfigParser.py
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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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getLaneAndSequenceInfo.py
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Grabs average SNP calls, mismatch rate, aligned reads, and other important lane metrics from a SQUID export and summarizes them across multiple margins (lane numbers, flowcells, samples, libraries)
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2010-04-17 03:09:05 +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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igvController.py
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Now can take a VCF file as input
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2010-05-18 17:06:12 +00:00 |
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indelVerboseStats.py
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Minor improvements to simple python code
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2010-05-07 21:34:46 +00:00 |
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madPipelineUtils.py
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more powerful management routines for my pipeline
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2010-05-12 13:37:39 +00:00 |
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makeIGVCategory.py
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misc. useful updates to python library
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2010-06-30 16:33:32 +00:00 |
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makeIndelMask.py
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Removing unnecessary dependences that were causing problems for Sendu
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2010-05-21 13:07:41 +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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misc. useful updates to python library
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2010-06-30 16:33:32 +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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realignBamByChr.py
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misc. useful updates to python library
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2010-06-30 16:33:32 +00:00 |
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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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subsetDbSNPWithrsIDs.py
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simple tool that takes two dbSNP files and subsets the seconds to only include rsID SNPs present in the first. Used to make b129 against b37 by subsetting b131/b37 vs. b129/b36
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2010-05-12 13:39:09 +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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Minor improvements to simple python code
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2010-05-07 21:34:46 +00:00 |
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vcfReader.py
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misc. useful updates to python library
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2010-06-30 16:33:32 +00:00 |
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vcf_b36_to_hg18.py
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some useful routines for working with project processing. madPipeline contains a bunch of useful routines for building pipelines that I finally put into one file. Let's just say that I'm really looking forward to the new pipeline system...
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2010-04-26 12:34:04 +00:00 |
