| .. |
|
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
|
Fixes for VariantEval for genotyping mode
|
2009-09-18 21:01:43 +00:00 |
|
MergeBAMsUtils.py
|
Fixes for VariantEval for genotyping mode
|
2009-09-18 21:01:43 +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
|
Detects unmapped (no bai) bam files and doesn't blow up
|
2009-09-25 12:56:28 +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
|
Generalize the regexp for analysis files
|
2009-09-24 03:17:41 +00:00 |
|
callingProgress.py
|
simple monitor for watching pilot 1 call progress
|
2009-10-06 13:04:53 +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 |
|
expandedSummaryToVCF.py
|
Oops. Let's make sure only to write calls that the pool supports to the auxiliary vcf files.
|
2009-11-04 17:14:55 +00:00 |
|
faiReader.py
|
Better snpSelector, plus VCFmerge tool
|
2009-11-11 22:02:57 +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 |
|
mergeVCFInfoFields.py
|
Awful stupid bug. This will use up one of my bad code offsets.
|
2009-11-29 20:09:33 +00:00 |
|
mergeVCFs.py
|
Better snpSelector, plus VCFmerge tool
|
2009-11-11 22:02:57 +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 |
|
snpSelector.py
|
Better support for comparison to truth. Now emits FP rates for each covariate if a truth file is provided. Also now writes out a detailed recal.log file that can be parsed directly into R
|
2009-11-29 22:20:40 +00:00 |
|
tgtc2sam.py
|
Move non-java code out of playground.
|
2009-03-23 19:31:38 +00:00 |
|
vcf2table.py
|
Useful library for parsing VCF files, plus a general VCF->table converter
|
2009-11-03 13:14:04 +00:00 |
|
vcfReader.py
|
More informative printing, no longer prints tons of NaN warnings
|
2009-11-24 15:45:48 +00:00 |
2ea93385be