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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
76838673e5
some fixes
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1622 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-15 01:35:36 +00:00
0feee9cdfd
finished up modularized pipeline; needs some testing but is generally done.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1610 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-14 02:41:57 +00:00
84c8374e68
2nd stab at creating a pipeline [not quite finished yet].
...
Modularized the system to emulate what it will look like in firehose.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1605 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-13 05:53:18 +00:00
702ba553d6
Some useful scripts for running only individual parts of the pilot1/2 cleaning/calling pipeline
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1587 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-11 17:38:33 +00:00
dab7b6e825
A useful perl module for quick argument parsing.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1491 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-31 15:44:57 +00:00
5d155440cd
A useful, rule-based parallel job dispatcher.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1490 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-31 15:40:21 +00:00
843d7e6c8f
Now you can specify '-' instead of input file name, and the script will read from stdin
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1422 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-14 20:30:56 +00:00
8d06bb21ed
A little gadget to select random samples from input stream(s) of unknown length. By default, selects a single line (with probability 1/TOTAL_NUMBER_OF_LINES_READ), with -N option randomly selects specified number of lines. Can read from STDIN or from arbitrary number of input streams (all streams will be merged). Examples:\n cat file1 file2 file3 | randomSampleFromStream.pl -N 5 \n\n or \n randomSampleFromStream.pl file1 file2 file3
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1360 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-31 18:55:14 +00:00
1d84c9da96
sortByRef now supports x:y location syntax
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1186 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 16:42:40 +00:00
3098ed091c
checking in new folder for perl scripts AND a simple script that takes an input text file and reference dictionary (.fai) and performs stable sort of the input lines according to the contig order specified by the dictionary. Position of the contig filed to sort on in the input lines is specified as --k POS option. Input lines may specify contigs that are not in the dictionary, in this case the additional contigs will be added at the end of the sorted output, after all known contigs. The sorting order between these additional contigs is simply the order in which they first appear in the input
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@831 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 16:34:55 +00:00
hanna
kiran
ebanks
kshakir
asivache
andrewk
depristo