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263 Commits (72ad8ded194adaab3f931da20b583f5ca0cbfc06)

Author SHA1 Message Date
chartl 8a0e813b04 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) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5482 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-21 16:11:55 +00:00
chartl 4a09d25a90 One last little thing, I swear 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5423 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-11 17:37:40 +00:00
chartl be1f6af815 Let's go the other way. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5422 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-11 17:36:41 +00:00
chartl 572b2707f2 oops 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5421 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-11 17:34:27 +00:00
chartl aea0c733a4 A pilot for empirical recalibration of association scores. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5420 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-11 17:32:45 +00:00
depristo b1b9c14c98 Minor utility improvements 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5325 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-26 15:36:26 +00:00
chartl 44a48b4178 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 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5314 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-25 01:23:53 +00:00
chartl a081f3b94f Modifications, bugfix to theoretical posteriors. (Bug fix: eliminated discontinuity in prior distribution) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5239 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-14 19:47:34 +00:00
depristo 393df46055 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 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5157 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-01 12:02:12 +00:00
chartl f8609afd4e Committing two pieces of code for exome analysis, in case they need be returned to 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5135 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-31 14:13:09 +00:00
corin bccc71c481 updated to work with the new tearsheet 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5112 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-28 18:46:38 +00:00
corin 32cdcc933c A quick python script to give the status of the projects in the humgen/gsa-pipeline/ directory 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5070 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-25 15:21:50 +00:00
depristo e64a300642 Deleting old python code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4961 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-07 21:33:45 +00:00
depristo 3362f0c280 Private mutation simulator and analysis routines for EOMI paper 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4960 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-07 21:23:29 +00:00
depristo 2448b859e4 no longer prints unnecessary table conversion failures that muck up emails. Run script now uses du not ls to display archive size 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4918 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-02 13:27:37 +00:00
depristo 501d44fa04 Minor bug fixee, replace double quotes with single quotes in strings so that R can read the resulting table 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4910 348d0f76-0448-11de-a6fe-93d51630548a
 2010-12-29 16:25:59 +00:00
depristo 46cd227613 Stabilitity improvements to GATK run report system. R code is now robust. XML parser uses the C backend in python, 10x faster. Added shell script that runs the daily reports, and linked the /humgen/ runme.csh to this script. Script now emails the group the daily PDFs to gsamembers 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4845 348d0f76-0448-11de-a6fe-93d51630548a
 2010-12-15 14:56:12 +00:00
depristo fabb42924c 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 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4810 348d0f76-0448-11de-a6fe-93d51630548a
 2010-12-09 04:44:16 +00:00
depristo 984e94521e Trival changes to data processing paper python 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4762 348d0f76-0448-11de-a6fe-93d51630548a
 2010-12-01 14:57:14 +00:00
depristo 187b464ded calling pipeline for v13 of the paper calls -- the final version 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4716 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-22 21:57:12 +00:00
depristo 0e062ae040 V1 of the data processing paper, produced results for the manuscript we presented. Commit for archival purposes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4648 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-11 01:43:21 +00:00
depristo fc39377e6c Simple pre-processing script for soapsnp files 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4627 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-04 20:34:43 +00:00
depristo 16c64558b4 Commenting out annoying print statement 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4566 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-24 11:55:26 +00:00
depristo 9fcfd8fa0d analyzeRunReports now actually implements no-dev 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4557 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 19:53:23 +00:00
ebanks ccc22c2331 Adding a script to do big table conversion. Removing Ben's script which is totally obsolete and busted. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4480 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-12 01:40:43 +00:00
depristo 04b4adafda File reports are now sorted in order 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4447 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-06 21:54:23 +00:00
depristo effcd26977 Shorter outputs, new summary mode 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4440 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-06 14:34:50 +00:00
aaron cfebe5c731 clean-up the docs a little 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4375 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 05:02:41 +00:00
aaron 702449d835 adding a Python script to roll back tribble to the correct version, for users who want to checkout historical versions of the GATK code. This code cross references the current checkout date with the Tribble logs, and pulls the closest (price-is-right style) revision. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4374 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 05:01:46 +00:00
chartl 37613810bf Tired of writing vcf_hg18_to_b36 over and over again when necessary. Added a -r flag to this script that does it. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4363 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-28 14:51:57 +00:00
chartl 40274ba7dc Do this the right way 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4310 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-19 04:30:48 +00:00
chartl fa8cfd3031 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/ 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4309 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-19 02:45:16 +00:00
depristo b57a0a0310 improvements to the report code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4280 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 00:45:13 +00:00
depristo 5de1124997 more useful reports 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4259 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 14:03:44 +00:00
depristo c524a9ec83 Minor usability improvements to reporting tool 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4224 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 02:56:25 +00:00
depristo 924e16f4f0 More robust analysis tool 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4187 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-01 20:24:04 +00:00
depristo 0c54bf4195 Better reporting and now with a special mode for listing exceptions 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4183 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-01 16:19:51 +00:00
depristo fc5caa98a5 Improved reporting now with metrics by day/week/etc. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4180 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-01 02:43:13 +00:00
depristo 8683087756 Suppl. tools for working with and displaying GATK run reports 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4176 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-31 20:32:22 +00:00
depristo 9556004dbb now supports -o option as well as verbose output mode 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4162 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-29 16:00:00 +00:00
kiran 7671502e1b Changes from James Pirruccello: now can handle differences between UCSC and NCBI tables, properly sorting despite the contig prefix differences (presence or absence of 'chr'), and converts NCBI format to UCSC format for use by the GenomicAnnotator. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4132 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-26 19:02:29 +00:00
corin 83624e3af3 updated to deal with new cleaning pipeline outputs and potentially infinity TI/TV 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4098 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-24 16:01:09 +00:00
depristo 669d9096e3 now support -o output option, useful for pipelines 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3959 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-06 14:57:04 +00:00
chartl 6dcb63888d Be smart about the headers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3912 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-30 16:11:16 +00:00
chartl eeb767a012 Remove legacy "out" 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3911 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-30 15:01:02 +00:00
chartl f20cdbe60a Modified to work with MT containing VCFs. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3910 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-30 14:59:59 +00:00
chartl 52f24c86fa Script to split a provided interval list into contigs. Excesses will be dropped into the last provided file. Works like splitIntervals.sh. This is for Queue. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3895 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-29 16:42:53 +00:00
corin 3596b1529f module for listing out samples for data processing and firehose reporting 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3847 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-21 15:05:41 +00:00
corin 1209b165bf Now accepts command line args and prints paths to vcf, bams and beds 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3846 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-21 15:04:58 +00:00
depristo 2bdb011865 Improvements to 1KG processing pipeline 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3807 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-16 15:33:47 +00:00