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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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CoverageEval.py
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Lot of code for coverage evaluation tools including first version of python script to evaluate the downsampled SSG callls made and the java code to make all the calls at Hapmap chip sites at various downsampling levels; ListUtils contains functions for randomnly subsetting lists (with replacement) which are useful for subsetting the same elements in both the reads and the offsets lists of a LocusWalker
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2009-07-03 08:07:02 +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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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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Version 0.2.1 (released) of the TableRecalibrator
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2009-06-25 22:50:55 +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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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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Slightly improved interface to merging utility for multiple bam files
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2009-05-20 12:54:41 +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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Version 0.2.1 (released) of the TableRecalibrator
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2009-06-25 22:50:55 +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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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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farm_commands.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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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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Major improvements to python analysis code -- now computes a host of statistics about quality scores from the recal_data.csv file emitted by countcovariates. Includes average Q scores, medians, modes, stdev, coefficients of variation, RSME, and % bases > q10, q20, q30. Can finally quantify and compare the improvement of quality score recalibration.
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2009-06-20 19:50:37 +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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Version 0.2.1 (released) of the TableRecalibrator
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2009-06-25 22:50:55 +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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