depristo d665d9714f By default now writes output to JOBID.lsf.output instead of going to email -- based on recommendations from the cancer group ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1325 348d0f76-0448-11de-a6fe-93d51630548a		2009-07-28 13:18:58 +00:00
..
AlignBam.py	Script that aligns paired-end BAMs using BWA.	2009-06-18 18:14:58 +00:00
CoverageEval.py	CoverageEval.py tool right before some major changes to the core of the code	2009-07-22 16:58:23 +00:00
EvalMapping.py	…
FastaQuals2Fastq.py	…
FlatFileTable.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
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	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
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	…
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
SAM.py	Better merge support	2009-05-18 21:18:51 +00:00
SamWalk.py	…
SamWalkTest.py	…
SimpleSAM.py	…
SimulateReads.py	Actually writes out a good header now	2009-05-18 13:34:52 +00:00
SpawnMapperJobs.py	…
SpawnValidationJobs.py	…
StressTestGATK.py	…
ValidateGATK.py	Actually listens to justPrint now	2009-07-15 16:52:46 +00:00
WalkLociTest.py	…
Walker.py	…
aln_file.nocvs.py	…
aln_file.py	…
analyzeRecalQuals.py	Updated python files	2009-07-07 14:15:39 +00:00
compSNPCalls.py	…
countCoverageWithSamtools.py	…
easyRecalQuals.py	Updated python files	2009-07-07 14:15:39 +00:00
farm_commands.py	By default now writes output to JOBID.lsf.output instead of going to email -- based on recommendations from the cancer group	2009-07-28 13:18:58 +00:00
fasta.py	…
gatkConfigParser.py	Updated python files	2009-07-07 14:15:39 +00:00
memo.py	…
picard_utils.py	Updated python files	2009-07-07 14:15:39 +00:00
pushback_file.py	…
qltout.py	…
samtooltest.sh	…
tgtc2sam.py	…