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AlignBam.py
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Script that aligns paired-end BAMs using BWA.
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2009-06-18 18:14:58 +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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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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Skip compiled python files (*.pyc) in svn status output
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2009-07-30 21:45:23 +00:00 |
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CoverageMeta.py
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Script that runs most of the steps involved in validating the CoverageEval system that predicts performance for given depth of sequencing coverage across a genome.
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2009-07-31 00:18:45 +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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Skip compiled python files (*.pyc) in svn status output
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2009-07-30 21:45:23 +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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Much improved python analysis routines, as well as easier / more correct merging utility. Better R scripts, which now close recalibration data by the confidence of the quality score itself
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2009-06-24 01:12:35 +00:00 |
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MergeBAMsUtils.py
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Much improved python analysis routines, as well as easier / more correct merging utility. Better R scripts, which now close recalibration data by the confidence of the quality score itself
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2009-06-24 01:12:35 +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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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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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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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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analyzeRecalQuals.py
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Updated python files
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2009-07-07 14:15:39 +00:00 |
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analyzeRecalQuals_1KG.py
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I've pulled out the functionality of the analyzer into a single python file which doesn't require all of the irrelevant config parameters (which would cause problems for external users). I'll release this and the simple config file to 1KG for use in analyzing recalibration efforts.
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2009-08-11 02:56:43 +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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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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farm_commands.py
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By default now writes output to JOBID.lsf.output instead of going to email -- based on recommendations from the cancer group
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2009-07-28 13:18:58 +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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Updated python files
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2009-07-07 14:15:39 +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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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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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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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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