zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
4,655 Commits
1 Branch
0 Tags
257 MiB
Commit Graph

60 Commits (d492eb94ad2bb7e5c79a4d9cd051feca3abfd8a7)

Author SHA1 Message Date
corin f8e1ea7b64 Script based on the second part of Eric's createTranscriptToGenomicInfoTables.pl script which sorts flat files by reference order 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4682 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-15 19:44:32 +00:00
asivache f2ee5dc319 regexp fixed, now can find OBS_COUNTS followed by both [C/A/R] (obsolete) and [C/A/T] (current) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4675 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-15 15:28:38 +00:00
kshakir 990677ec36 Also removed contig intervals from the pipeline sanity check perl scsript. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4540 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-21 11:23:34 +00:00
ebanks c305b41da4 Patch for James 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4526 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 02:39:16 +00:00
ebanks f962039273 Using James P's patch for the liftover script 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4515 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-18 01:44:54 +00:00
ebanks e6d038067b cleanup the temp index too 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4512 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-17 04:41:42 +00:00
ebanks 7aa030a9a4 Hmm. Apparently variants can get lifted over to different chromosomes. Who knew? Reverting changes from a couple of days ago. The only way to do this correctly (without requiring lots of memory) is to turn off on-the-fly indexing for this walker. Integration tests cover this now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4510 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-17 02:54:12 +00:00
kshakir 196029c0b4 Removed obsolete -bsubWait from sanity check. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4509 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-16 02:14:34 +00:00
ebanks 3d988576a6 updated liftover script: it no longer needs to re-sort the vcf 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4501 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-15 08:03:41 +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
ebanks 7f1e44b764 update the example: /broad/1KG doesn't exist anymore 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4429 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-05 13:50:24 +00:00
kiran a15757b8e8 Obsoleted by VariantReport.R 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4418 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-04 01:00:59 +00:00
kiran a90fb64c03 Added 'Cron' to subject for easier message filtering 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4366 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-28 21:03:50 +00:00
kiran a7815b4268 Nightly test for Queue-based pipeline. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4358 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-27 05:24:58 +00:00
hanna 5119bdb55e - Update DoC to support output to /dev/null. 
- Add a release sanity check for DoC.
- Update release sanity checks with new command-line argument system.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4236 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 23:43:18 +00:00
kiran 84ddadca64 One more fix: exclude input VCF file's directory name from the output file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4226 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 03:09:08 +00:00
kiran bd878565f6 Change for Firehose: infers output path from the input VCF, so that we don't have to change a whole bunch of stuff so that Firehose knows where to expect the output file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4221 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-07 21:07:46 +00:00
kiran e9af893bf4 Write headers that are VCF4.0 compliant 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4213 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-03 23:46:27 +00:00
ebanks 3d6c4fc55f Removing the obsolete --hapmap and --hapmap_chip options 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4172 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-31 16:57:05 +00:00
ebanks a7af605d95 update to use new rod syntax 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4119 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-25 20:21:53 +00:00
kiran 1c3f2be829 Change for Chris: don't depend on other Perl modules. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4053 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-17 22:19:13 +00:00
ebanks 86bd55408e no INFO output now that it's the default 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4014 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-11 18:56:28 +00:00
kiran 23b5d71e76 A quickly hacked together replacement for AnnotateVCFwithMAF.py, which doesn't work anymore with Cancer's updated annotator. Takes an annotated MAF file and imports the annotations into the VCF file. For the MAF annotator's DNP and TNP annotations (which I think are likely to not be correct, given the lack of phasing information or even proper association to the same sample), just propagate the annotation from the previous annotated variant to which the multinucleotide polymorphism was associated. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4007 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-11 00:20:08 +00:00
ebanks e50627a49e 1. Updated tests and added integration test for liftover code. 
2. Updated liftover code (and scripts) to emit vcf 4.0 and no longer depend on VCFRecord.
3. Beagle walker now also emits vcf 4.0.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3767 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-12 17:58:18 +00:00
kshakir c80a257f37 Updated for CentOS changes. 
See: http://iwww.broadinstitute.org/itsystems/wiki/Dotkit#Job_Specific_Wrapper_Script


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3742 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-08 14:36:24 +00:00
ebanks 6a0483ee95 fixed typos 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3729 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-07 17:41:44 +00:00
ebanks 2ac74a862d updated to deal with new cleaner options 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3728 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-07 17:06:00 +00:00
ebanks 15a6be5d50 Updated to reflect Mark's renaming binge 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3697 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-30 22:48:42 +00:00
kiran 26ef1f84bf Updates to not depend on an environment variable to figure out where libraries are (helpful for installation at the Sanger). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3655 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-28 15:46:41 +00:00
kiran b2127e59c4 A first draft of scripts and LaTeX templates required to automatically generate slides for the 1,000 Genomes Automated Data Processing Report. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3652 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-28 14:30:50 +00:00
asivache 17d2043354 bug fix: now contigs not present in the sequence dictionary are registered properly and do not cause the script to break 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3623 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-23 20:59:38 +00:00
ebanks 22abbc0edb Stupid cent_os doesn't allow old style 'sort' conventions. Updating liftover script... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3577 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-17 13:44:03 +00:00
ebanks a0bf1753f9 A script to sanity check that a release is runnable. 
Not fancy - just pulls out the performance tests in 20sec chunks.  Only a temporary solution.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3442 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-26 17:45:42 +00:00
ebanks 7cab994d88 Add argument to sortByRef for specifying the tmp directory for sorting. 
Update the liftover script to reflect this addition.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3323 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 13:53:26 +00:00
ebanks bfc58c70fa Adding newline 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3322 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 13:08:08 +00:00
ebanks 44de92e09d Checking in the liftover script. I am including a post-processing walker to filter out bad records written in under 10 minutes as per my agreement with Mark. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3321 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 12:31:56 +00:00
ebanks ca649d13aa Adding the post-processing indel filter to GATK 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3263 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-27 14:43:39 +00:00
kshakir 4965d6b26a Passing just the single alternate allele to the converted maf on the recommendation of mike lawrence and kiran. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3026 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 19:08:37 +00:00
kiran 1e170369b9 A quick module to load up text files more easily 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2988 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 02:31:29 +00:00
kshakir 8f4fbf29a7 Band-Aid: changed the pointers from mike's home directory to a checkout of the last know working revision r7169 in my directory. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2946 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-07 04:19:01 +00:00
kiran f859e14cc7 Allow no-call alleles to propagate through to the MAF file 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2848 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-16 20:46:16 +00:00
kiran d4e4120ca1 Some useful changes that I've had laying around for a while - deletes files from failed runs, automatically adds a memory limit to java commands where one isn't specified, and touches files on the local machine after command completion to get around the problem with the times not being perfectly synchronized across LSF nodes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2829 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 00:18:34 +00:00
andrewk fdc2789322 Minor fix: removed use command that doesn't work in /bin/sh scripts. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2799 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 19:52:50 +00:00
andrewk 58456822ab Two perl scripts (from Kristian Cibulskis) and one python script for annotating VCF files with the information generated by the cancer MAF annotation tool. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2797 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 19:25:46 +00:00
ebanks 8461cc3a22 /tmp is failing... 
We should be using hptmp anyways.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1793 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 18:13:49 +00:00
ebanks b39a307a04 SSG -> UG 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1790 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 17:40:09 +00:00
ebanks e9eeed8c6f add wait id for 454 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1678 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-22 01:41:58 +00:00
ebanks d9ee515a9b rename some jobnames so that LSF doesn't complain 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1657 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 19:02:15 +00:00
ebanks 4c89140f21 quick fix 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1655 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 18:17:13 +00:00
ebanks 598974ae10 perl script to make batching jobs easier 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1638 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-16 19:02:46 +00:00