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andrewk d191e02c88 Automated parsing stats from VariantEval and outputting stats to "*.oneline_stats" files; needed to do larger culling of predictions vs. actual SNP call for Pilot 3 lanes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1620 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-09-14 23:40:11 +00:00
..
1kgScripts update script to put pilot1 bams directly onto hphome 2009-09-08 14:41:35 +00:00
AlignBam.py Give usage message if no arguments provided. 2009-08-31 00:28:43 +00:00
AlignBams.py Short python script that takes paired-end BAMs and aligns them with BWA. Referenced in GSA wiki tutorial 2009-07-31 00:04:10 +00:00
BarcodeAnalysis.py Added command line options to make the barcode analysis script executable by end users. 2009-08-24 21:15:09 +00:00
CoverageEval.py Automated parsing stats from VariantEval and outputting stats to "*.oneline_stats" files; needed to do larger culling of predictions vs. actual SNP call for Pilot 3 lanes 2009-09-14 23:40:11 +00:00
CoverageMeta.py Many generalization improvements - parameters, files as options - to script that runs pieces for predicting SNP calling performance for given SNP calling coverage 2009-09-14 23:37:53 +00:00
DOCParameter.py Checking in Michael's DoC parameterization script; 2009-09-03 15:07:49 +00:00
EvalMapping.py Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
FastaQuals2Fastq.py Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
FlatFileTable.py Skip compiled python files (*.pyc) in svn status output 2009-07-30 21:45:23 +00:00
Geli2GFF.py Updated coverter to reflect change in contig ordering in Geli files 2009-06-03 10:05:28 +00:00
Gelis2PopSNPs.py Fixing odd merge problem with VariantEval -- better cluster analysis (no cumsum), rodVariant is now an AllelicVariant 2009-07-14 18:53:27 +00:00
LogRegression.py Merged functionality of two python scripts into LogRegression.py, some clarity updates to covariate and regression java files. 2009-06-02 16:55:05 +00:00
LogisticRegressionByReadGroup.py Revert some debug code in RecalQual.py. Make LogisticRegression easier to Ctrl-C out of. 2009-06-05 01:53:48 +00:00
MergeBAMBatch.py LocusIterationByState is now the system deafult. Fixed Aaron's build problem 2009-09-09 01:28:05 +00:00
MergeBAMsUtils.py 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 2009-06-24 01:12:35 +00:00
MergeBamsByKey.py Trivial change 2009-06-12 19:11:28 +00:00
MergeEvalMapTabs.py Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
ParseDCCSequenceData.py 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. 2009-07-08 22:04:26 +00:00
RecalQual.py Updated version of the recalibration tool 2009-06-19 17:45:47 +00:00
RunPilot2Pipeline.py Fix merger command 2009-09-11 13:13:23 +00:00
SAM.py Better merge support 2009-05-18 21:18:51 +00:00
SamWalk.py Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
SamWalkTest.py Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
SimpleSAM.py Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
SimulateReads.py Actually writes out a good header now 2009-05-18 13:34:52 +00:00
SpawnMapperJobs.py Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
SpawnValidationJobs.py Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
StressTestGATK.py 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. 2009-04-14 22:13:10 +00:00
ValidateGATK.py Actually listens to justPrint now 2009-07-15 16:52:46 +00:00
Verify1KGArchiveBAMs.py Framework for ROD walkers -- totally experiment and not working right now 2009-09-12 19:13:15 +00:00
WalkLociTest.py Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
Walker.py Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
aln_file.nocvs.py Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
aln_file.py Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
analyzeRecalQuals.py Updated python files 2009-07-07 14:15:39 +00:00
analyzeRecalQuals_1KG.py 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. 2009-08-11 02:56:43 +00:00
compSNPCalls.py Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
countCoverageWithSamtools.py Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
easyRecalQuals.py Updated python files 2009-07-07 14:15:39 +00:00
farm_commands.py Added die_on_fail which outputs an error message and stops execution if a farm or terminal command fails 2009-09-14 23:30:13 +00:00
fasta.py Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
gatkConfigParser.py High performance LocusIterator implementation. Now with greatly reduced memory impact and 2x (and more potentially) speed ups of raw locus iteration. General performance improvements to SSG with empirical probs. You can enable high-performance locus iteration with the -LIBS arg. It's still testing but passes validing pileup. 2009-09-03 03:06:25 +00:00
memo.py Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
picard_utils.py Updated python files 2009-07-07 14:15:39 +00:00
pushback_file.py Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
qltout.py Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
samtooltest.sh Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
tgtc2sam.py Move non-java code out of playground. 2009-03-23 19:31:38 +00:00