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genomicAnnotatorScripts
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Adding a script to do big table conversion. Removing Ben's script which is totally obsolete and busted.
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2010-10-12 01:40:43 +00:00 |
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1kgStatsForCalls.py
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Better reporting and now with a special mode for listing exceptions
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2010-09-01 16:19:51 +00:00 |
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AnnotateVCFwithMAF.py
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Restore "type" annotation (but not genomechange or cDNA change, which are already encoded in the VCF)
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2010-07-13 17:33:15 +00:00 |
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JobDispatcher.py
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Memory string added
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2010-07-12 20:43:19 +00:00 |
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JobDispatcherExample.py
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This is a python job dispatcher I've been using, which builds on Mark's FarmJob utility, and an example script of how I'm using it. Basically I wrote it to smartly break up analysis over an interval list, givin a maximum number of bases per job, a list of available queues, and a limit on each queue. It handles going over these limits in three ways:
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2010-03-31 19:53:13 +00:00 |
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MPGQueuePipelineStatus.py
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updated to work with the new tearsheet
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2011-01-28 18:46:38 +00:00 |
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ParseDCCSequenceData.py
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RefseqLibrary.py
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Awesome: JobDispatcher can now dispatch jobs by gene from a target .design file found in /seq/references.
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2010-04-14 18:17:41 +00:00 |
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RunPilot2Pipeline.py
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SyzygyCallsFileToVCF.py
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VCFValidationAnalysis.py
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Verify1KGArchiveBAMs.py
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Minor utility improvements
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2011-02-26 15:36:26 +00:00 |
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analyzeRunReports.py
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updates to handle only reporting on a specific SVN revision. Updated the R script to show the domain name of the runner, now that S3 logging is working
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2011-02-01 12:02:12 +00:00 |
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collectCalls.py
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countCoverageWithSamtools.py
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createCaseControlMetaData.py
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A helper script that will take a list of bams, a list of case sample IDs, and a list of control sample IDs, and generate a sample meta data yaml (which includes the bamfiles)
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2011-03-21 16:11:55 +00:00 |
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dataProcessingPaper.py
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Trival changes to data processing paper python
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2010-12-01 14:57:14 +00:00 |
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expandedSummaryToVCF.py
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faiReader.py
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farm_commands.py
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farm_commands2.py
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Minor improvements to my crappy old python job management system. Mauricio's first task is to retire all of this code and move the DPP pipeline over to Queue
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2010-12-09 04:44:16 +00:00 |
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fasta.py
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firehose_out_email.py
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updated to deal with new cleaning pipeline outputs and potentially infinity TI/TV
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2010-08-24 16:01:09 +00:00 |
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fixSoapSnp.py
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Simple pre-processing script for soapsnp files
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2010-11-04 20:34:43 +00:00 |
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gatherIndelsToVCF.py
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Adding this to get around lsf/csh issues (see recent help message). Also seems like a good time to reiterate http://www.faqs.org/faqs/unix-faq/shell/csh-whynot/
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2010-09-19 02:45:16 +00:00 |
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gatherSampleSummaries.py
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If you scatter depth of coverage and need to do something more sophisticated than gathering up (e.g. concatenating) the interval summary file, and need to smartly gather up a full summary file, modify (stress on MODIFY) this script to do it
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2011-02-25 01:23:53 +00:00 |
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gatkConfigParser.py
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generate1KGHapmapVCF.py
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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.
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2010-01-28 21:59:33 +00:00 |
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getBamFilesFromSpreadsheet.py
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Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics
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2010-03-29 13:32:00 +00:00 |
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getLaneAndSequenceInfo.py
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Grabs average SNP calls, mismatch rate, aligned reads, and other important lane metrics from a SQUID export and summarizes them across multiple margins (lane numbers, flowcells, samples, libraries)
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2010-04-17 03:09:05 +00:00 |
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getTargetedGenes.py
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Just some code I want to freeze. If you ever need to estimate the % of bases covered by exon, given an interval list, give it to getTargetedGenes. Not the best name for this function, but I don't expect anyone to use it but me.
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2010-04-01 20:21:50 +00:00 |
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igvController.py
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Now can take a VCF file as input
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2010-05-18 17:06:12 +00:00 |
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indelVerboseStats.py
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Minor improvements to simple python code
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2010-05-07 21:34:46 +00:00 |
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lsf_post_touch.py
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Do this the right way
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2010-09-19 04:30:48 +00:00 |
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madPipelineUtils.py
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Minor improvements to my crappy old python job management system. Mauricio's first task is to retire all of this code and move the DPP pipeline over to Queue
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2010-12-09 04:44:16 +00:00 |
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makeIndelMask.py
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Removing unnecessary dependences that were causing problems for Sendu
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2010-05-21 13:07:41 +00:00 |
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makeMetricsFilesForFirehose.py
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Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics
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2010-03-29 13:32:00 +00:00 |
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memo.py
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mergeVCFInfoFields.py
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Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics
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2010-03-29 13:32:00 +00:00 |
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picard_utils.py
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misc. changes to python scripts
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2010-07-09 00:13:35 +00:00 |
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privateMutationRates.py
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Private mutation simulator and analysis routines for EOMI paper
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2011-01-07 21:23:29 +00:00 |
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pushback_file.py
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realignBamByChr.py
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Improvements to 1KG processing pipeline
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2010-07-16 15:33:47 +00:00 |
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recalAssociation.py
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One last little thing, I swear
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2011-03-11 17:37:40 +00:00 |
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sample_lister.py
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module for listing out samples for data processing and firehose reporting
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2010-07-21 15:05:41 +00:00 |
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setFilterGenotypesToRef.py
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Quick python scripts for going from genotype VCFs to site-only VCFs, and one to fix BC vcf files (which had "het" genotypes at non-variant sites)
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2010-07-12 19:13:32 +00:00 |
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splitIntervalsByContig.py
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Adding this to get around lsf/csh issues (see recent help message). Also seems like a good time to reiterate http://www.faqs.org/faqs/unix-faq/shell/csh-whynot/
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2010-09-19 02:45:16 +00:00 |
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theoPost.py
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Modifications, bugfix to theoretical posteriors. (Bug fix: eliminated discontinuity in prior distribution)
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2011-02-14 19:47:34 +00:00 |
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ucscRepeatMaskToIntervalList.py
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better farm commands, and simple utility to convert ucsc repeat masks to interval lists
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2010-03-19 13:11:06 +00:00 |
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updateTribbleToCorrectSVNVersion.py
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clean-up the docs a little
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2010-09-29 05:02:41 +00:00 |
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validatePosterior.py
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Committing two pieces of code for exome analysis, in case they need be returned to
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2011-01-31 14:13:09 +00:00 |
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vcf2table.py
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now support -o output option, useful for pipelines
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2010-08-06 14:57:04 +00:00 |
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vcfGenotypeToSites.py
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Quick python scripts for going from genotype VCFs to site-only VCFs, and one to fix BC vcf files (which had "het" genotypes at non-variant sites)
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2010-07-12 19:13:32 +00:00 |
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vcfReader.py
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now support -o output option, useful for pipelines
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2010-08-06 14:57:04 +00:00 |
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vcf_b36_to_hg18.py
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Tired of writing vcf_hg18_to_b36 over and over again when necessary. Added a -r flag to this script that does it.
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2010-09-28 14:51:57 +00:00 |
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