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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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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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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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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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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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Detects unmapped (no bai) bam files and doesn't blow up
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2009-09-25 12:56:28 +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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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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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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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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Check to ensure sample status is "Complete" before writing out the bam file
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2010-02-16 15:36:42 +00:00 |
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makeMetricsFilesForFirehose.py
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Dumb little script that grabs Picard metrics (alignment, hybrid selection, insert size) from picard_aggregation given the path to the bam file; zips them up, and spits them out; for use with Firehose
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2010-02-11 14:09:30 +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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Awful stupid bug. This will use up one of my bad code offsets.
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2009-11-29 20:09:33 +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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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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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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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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Move non-java code out of playground.
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2009-03-23 19:31:38 +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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