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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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10x speedup of recalibration walker
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2009-06-09 15:39:40 +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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more and better python scripts for dealing with calls
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2009-06-02 20:37:19 +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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Allow script to be easily modified to support different platforms.
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2009-06-09 16:06:57 +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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major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps.
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2009-06-05 23:34:37 +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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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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10x speedup of recalibration walker
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2009-06-09 15:39:40 +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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