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EvalMapping.py
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2009-03-23 19:31:38 +00:00 |
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FastaQuals2Fastq.py
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2009-03-23 19:31:38 +00:00 |
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Geli2GFF.py
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Added Hapmap data track (using rodGFF class for GFF file format) to toolkit as a command line option, Hapmap metrics to AlleleFrequencyMetricsWalker, and a python Geli2GFF file converter.
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2009-03-24 03:58:03 +00:00 |
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LogRegression.py
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LogRegression.py script that converts parameter files for each dinucleotide regression into one file to be read in by correction script.
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2009-04-24 18:31:26 +00:00 |
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MergeBAMBatch.py
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Support for indexBAM command
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2009-04-22 19:39:07 +00:00 |
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MergeEvalMapTabs.py
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2009-03-23 19:31:38 +00:00 |
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SAM.py
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2009-03-23 19:31:38 +00:00 |
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SamWalk.py
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2009-03-23 19:31:38 +00:00 |
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SamWalkTest.py
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2009-03-23 19:31:38 +00:00 |
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SimpleSAM.py
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2009-03-23 19:31:38 +00:00 |
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SimulateReads.py
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2009-03-23 19:31:38 +00:00 |
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SpawnMapperJobs.py
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2009-03-23 19:31:38 +00:00 |
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SpawnValidationJobs.py
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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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Basic logistic regression support for calibrating qualities; mostly for Andrew to experiment with
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2009-04-24 19:09:50 +00:00 |
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WalkLociTest.py
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2009-03-23 19:31:38 +00:00 |
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Walker.py
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2009-03-23 19:31:38 +00:00 |
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aln_file.nocvs.py
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2009-03-23 19:31:38 +00:00 |
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aln_file.py
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2009-03-23 19:31:38 +00:00 |
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compSNPCalls.py
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2009-03-23 19:31:38 +00:00 |
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countCoverageWithSamtools.py
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2009-03-23 19:31:38 +00:00 |
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farm_commands.py
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Fixed potential bug with next() operation returning empty contexts when a read contains a large deletion. We can now use the look ahead safely...
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2009-04-15 21:41:30 +00:00 |
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fasta.py
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2009-03-23 19:31:38 +00:00 |
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memo.py
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2009-03-23 19:31:38 +00:00 |
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pushback_file.py
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2009-03-23 19:31:38 +00:00 |
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qltout.py
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2009-03-23 19:31:38 +00:00 |
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samtooltest.sh
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2009-03-23 19:31:38 +00:00 |
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tgtc2sam.py
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2009-03-23 19:31:38 +00:00 |
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