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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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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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Updated version of the recalibration tool
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2009-06-19 17:45:47 +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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10x speedup of recalibration walker
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2009-06-09 15:39:40 +00:00 |
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MergeBAMsUtils.py
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10x speedup of recalibration walker
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2009-06-09 15:39:40 +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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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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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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Updated version of the recalibration tool
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2009-06-19 17:45:47 +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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Now does really neightbor distance calculation, as well as true snp cluster counting
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2009-06-12 16:29:26 +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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recal_qual.py
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Added R script and uncommented a line in recal_qual.py
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2009-06-03 03:15:45 +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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