| .. |
|
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 |
|
AnnotateVCFwithMAF.py
|
Make annotated VCF not be broken
|
2010-03-01 23:22:41 +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
|
Updated SNP calling power from coverage tools to work with new UnifiedGenotyper and DepthOfCoverage tools.
|
2009-12-16 20:44:30 +00:00 |
|
CoverageMeta.py
|
Updated SNP calling power from coverage tools to work with new UnifiedGenotyper and DepthOfCoverage tools.
|
2009-12-16 20:44:30 +00:00 |
|
DOCParameter.py
|
Checking in Michael's DoC parameterization script;
|
2009-09-03 15:07:49 +00:00 |
|
EvalMapping.py
|
…
|
|
|
FastaQuals2Fastq.py
|
…
|
|
|
FlatFileTable.py
|
Add ability for flat file table parsing module to skip ahead to first occurence of a regular expression (use case: consistently parsing DepthOfCoverage output for histogram section of file across file format changes)
|
2009-12-16 20:38:50 +00:00 |
|
Geli2GFF.py
|
…
|
|
|
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
|
…
|
|
|
LogisticRegressionByReadGroup.py
|
…
|
|
|
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
|
…
|
|
|
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 |
|
RunPilot2Pipeline.py
|
Fix merger command
|
2009-09-11 13:13:23 +00:00 |
|
SAM.py
|
…
|
|
|
SamWalk.py
|
…
|
|
|
SamWalkTest.py
|
…
|
|
|
SimpleSAM.py
|
…
|
|
|
SimulateReads.py
|
…
|
|
|
SpawnMapperJobs.py
|
…
|
|
|
SpawnValidationJobs.py
|
…
|
|
|
StressTestGATK.py
|
…
|
|
|
SyzygyCallsFileToVCF.py
|
Minor changes (additional info calculated)
|
2010-01-06 16:41:01 +00:00 |
|
VCFValidationAnalysis.py
|
A collection of python objects that are useful for VCF validation. Use 'em or don't.
|
2010-01-25 18:44:10 +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
|
…
|
|
|
Walker.py
|
…
|
|
|
aln_file.nocvs.py
|
…
|
|
|
aln_file.py
|
…
|
|
|
callingProgress.py
|
simple monitor for watching pilot 1 call progress
|
2009-10-06 13:04:53 +00:00 |
|
collectCalls.py
|
Adding this to subversion so it's protected
|
2009-12-09 21:26:17 +00:00 |
|
compSNPCalls.py
|
…
|
|
|
countCoverageWithSamtools.py
|
…
|
|
|
create_venn_evals.py
|
Script to split concordance files into their constituent sets and calculate summary stats from a concordance file - SNPs called and number in dbSNP
|
2010-03-12 22:20:44 +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
|
Now supports strings in command line for farm submission
|
2010-01-06 13:15:40 +00:00 |
|
farm_commands2.py
|
better farm commands, and simple utility to convert ucsc repeat masks to interval lists
|
2010-03-19 13:11:06 +00:00 |
|
fasta.py
|
…
|
|
|
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 |
|
generate1KGHapmapVCF.py
|
Quick script that changes "chr#" to "#" and "chrM" to "MT" and moves mitochondria to the end of the vcf; in accordance with the 1KG reference.
|
2010-01-28 21:59:33 +00:00 |
|
getBamFilesFromSpreadsheet.py
|
automatic generation of individual and individual set import files
|
2010-03-15 10:36:33 +00:00 |
|
makeMetricsFilesForFirehose.py
|
Dumb little script that grabs Picard metrics (alignment, hybrid selection, insert size) from picard_aggregation given the path to the bam file; zips them up, and spits them out; for use with Firehose
|
2010-02-11 14:09:30 +00:00 |
|
memo.py
|
…
|
|
|
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
|
new -a option does fast merging of already sorted files
|
2010-01-05 13:55:39 +00:00 |
|
picard_utils.py
|
Updated python files
|
2009-07-07 14:15:39 +00:00 |
|
pilot2CallingPipeline.py
|
keeping a backup
|
2010-01-31 15:36:25 +00:00 |
|
pushback_file.py
|
…
|
|
|
qltout.py
|
…
|
|
|
samtooltest.sh
|
…
|
|
|
snpSelector.py
|
snpSelector now supports min and max q scores.
|
2010-01-31 19:38:34 +00:00 |
|
tgtc2sam.py
|
…
|
|
|
ucscRepeatMaskToIntervalList.py
|
better farm commands, and simple utility to convert ucsc repeat masks to interval lists
|
2010-03-19 13:11:06 +00:00 |
|
vcf2table.py
|
updates to the python snp selector -- now sorts info fields and we stop printing unnecessary debugging info in vcf2table
|
2009-12-04 22:16:02 +00:00 |
|
vcfReader.py
|
minor improvements to snpSelector to work with hapmap chip VCF files
|
2009-12-13 17:59:32 +00:00 |
08d9ae403d