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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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Changes from James Pirruccello: now can handle differences between UCSC and NCBI tables, properly sorting despite the contig prefix differences (presence or absence of 'chr'), and converts NCBI format to UCSC format for use by the GenomicAnnotator.
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2010-08-26 19:02:29 +00:00 |
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1kgStatsForCalls.py
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Better reporting and now with a special mode for listing exceptions
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2010-09-01 16:19:51 +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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Restore "type" annotation (but not genomechange or cDNA change, which are already encoded in the VCF)
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2010-07-13 17:33:15 +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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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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FastaQuals2Fastq.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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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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Updated coverter to reflect change in contig ordering in Geli files
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2009-06-03 10:05:28 +00:00 |
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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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Memory string added
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2010-07-12 20:43:19 +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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Merged functionality of two python scripts into LogRegression.py, some clarity updates to covariate and regression java files.
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2009-06-02 16:55:05 +00:00 |
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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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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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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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Better merge support
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2009-05-18 21:18:51 +00:00 |
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SamWalk.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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SamWalkTest.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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SimpleSAM.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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SimulateReads.py
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Actually writes out a good header now
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2009-05-18 13:34:52 +00:00 |
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SpawnMapperJobs.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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SpawnValidationJobs.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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StressTestGATK.py
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General purpose pileup code -- you can use these features to obtain detailed pileup data from reads and offsets. Useful for all pileup based walkers. Expanded support for rodSAMPileup to enable the new ValidatingPileupWalker, which takes a samtools pileup output and checks that GATK gives identical output as samtools on a per base and per qual pileup. It's going to be a very useful validation tool.
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2009-04-14 22:13:10 +00:00 |
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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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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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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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Walker.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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aln_file.nocvs.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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aln_file.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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analyzeRunReports.py
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Shorter outputs, new summary mode
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2010-10-06 14:34:50 +00:00 |
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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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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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countCoverageWithSamtools.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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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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misc. changes to python scripts
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2010-07-09 00:13:35 +00:00 |
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fasta.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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firehose_out_email.py
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updated to deal with new cleaning pipeline outputs and potentially infinity TI/TV
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2010-08-24 16:01:09 +00:00 |
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gatherIndelsToVCF.py
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Adding this to get around lsf/csh issues (see recent help message). Also seems like a good time to reiterate http://www.faqs.org/faqs/unix-faq/shell/csh-whynot/
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2010-09-19 02:45:16 +00:00 |
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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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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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lsf_post_touch.py
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Do this the right way
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2010-09-19 04:30:48 +00:00 |
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madPipelineUtils.py
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Improvements to 1KG processing pipeline
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2010-07-16 15:33:47 +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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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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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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now supports -o option as well as verbose output mode
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2010-08-29 16:00:00 +00:00 |
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picard_utils.py
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misc. changes to python scripts
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2010-07-09 00:13:35 +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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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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qltout.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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realignBamByChr.py
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Improvements to 1KG processing pipeline
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2010-07-16 15:33:47 +00:00 |
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sample_lister.py
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module for listing out samples for data processing and firehose reporting
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2010-07-21 15:05:41 +00:00 |
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samtooltest.sh
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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setFilterGenotypesToRef.py
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Quick python scripts for going from genotype VCFs to site-only VCFs, and one to fix BC vcf files (which had "het" genotypes at non-variant sites)
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2010-07-12 19:13:32 +00:00 |
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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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splitIntervalsByContig.py
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Adding this to get around lsf/csh issues (see recent help message). Also seems like a good time to reiterate http://www.faqs.org/faqs/unix-faq/shell/csh-whynot/
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2010-09-19 02:45:16 +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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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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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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updateTribbleToCorrectSVNVersion.py
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clean-up the docs a little
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2010-09-29 05:02:41 +00:00 |
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vcf2table.py
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now support -o output option, useful for pipelines
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2010-08-06 14:57:04 +00:00 |
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vcfGenotypeToSites.py
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Quick python scripts for going from genotype VCFs to site-only VCFs, and one to fix BC vcf files (which had "het" genotypes at non-variant sites)
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2010-07-12 19:13:32 +00:00 |
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vcfReader.py
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now support -o output option, useful for pipelines
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2010-08-06 14:57:04 +00:00 |
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vcf_b36_to_hg18.py
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Tired of writing vcf_hg18_to_b36 over and over again when necessary. Added a -r flag to this script that does it.
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2010-09-28 14:51:57 +00:00 |
effcd26977