fdc2ebb321
Adding ability to specify in VQSR a list of bad sites to use when training the negative model. Just add bad=true to the list of rod tags for your bad sites track.
2011-07-02 17:15:13 -04:00
09af6bbc6c
Ugh - backed out experimental code not for public consumption unintendedly committed
2011-07-02 16:58:57 -04:00
c6c0dba040
Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-02 16:45:34 -04:00
b66581dc45
More changes on consensus script
2011-07-02 16:45:08 -04:00
4532a84314
Merged bug fix from Stable into Unstable
2011-07-02 10:48:55 -04:00
14375c3ba9
Moving my very first walkers into the archive.
2011-07-02 10:45:12 -04:00
5faf40b79d
Moving AnalyzeAnnotations into the archive because it has outlived its usefulness.
2011-07-02 10:39:53 -04:00
43959e6780
Moving old R scripts into the archive
2011-07-02 10:33:27 -04:00
17ff5bb094
Variant records coming out of the VQSR are now annotated with which input annotation was most divergent from the Gaussian mixture model. This gives a general sense for why each variant was removed from the callset.
2011-07-02 09:55:35 -04:00
635dc5de4b
New hyper-parallel structure for indel consensus: each 3 MB chunk is divided into 100 subchunks so I can fit in hour queue. Got rid on indel realignment and snp parts, use BTI to compute only at input sites.
2011-07-01 20:51:01 -04:00
c65e52f88a
Merged bug fix from Stable into Unstable
2011-07-01 20:50:56 -04:00
b6bc64a0c8
Cleanup of the utils.broad package.
...
Using Picard IoUtils on sample names.
2011-07-01 20:47:03 -04:00
0c9105ca22
Minor fix of description
2011-07-01 18:07:35 -04:00
358cf98b67
Merged bug fix from Stable into Unstable
2011-07-01 17:27:07 -04:00
444eae316c
Moving these supported perl scripts to public
2011-07-01 17:26:25 -04:00
95abb2e14a
Merged bug fix from Stable into Unstable
2011-07-01 17:12:21 -04:00
cfdece6dd8
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-01 17:11:32 -04:00
1c1cd373d8
Fix to make liftOver.pl work with new file structure
2011-07-01 17:07:22 -04:00
a025f85c08
Merged bug fix from Stable into Unstable
2011-07-01 16:44:33 -04:00
546e7777fa
Re-fixing paths in pipeline tests after example qscripts got moved.
2011-07-01 16:39:10 -04:00
b19e22aed9
Merged bug fix from Stable into Unstable
2011-07-01 16:20:25 -04:00
e9030a7bfd
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-01 16:19:35 -04:00
d631f645c4
Merged bug fix from Stable into Unstable
2011-07-01 16:16:31 -04:00
b0fb63e20a
moving the example scala scripts to the qscripts package.
2011-07-01 16:14:59 -04:00
04971aecc9
Merged bug fix from Stable into Unstable
2011-07-01 16:04:50 -04:00
d647ea4fdc
Long-delayed change to CachingIndexedFastaSequenceFile. Made the cache
...
non-static to avoid problems when multiple references are used within the same
thread (eg., during integration tests). This should kill the intermittent
IndelRealignerIntegrationTest failures.
2011-07-01 16:04:30 -04:00
d19351f71a
Added capability of running multiple bam files in the same directory.
2011-07-01 16:02:28 -04:00
350a76d5dd
Merged bug fix from Stable into Unstable
2011-07-01 13:53:46 -04:00
11d4af0e75
Path-related fixes to the private queue pipeline tests.
2011-07-01 13:41:34 -04:00
9644f104c4
Fixes to the queue pipeline tests to account for the new directory structure.
2011-07-01 13:13:24 -04:00
7159b14e76
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-01 10:53:49 -04:00
bf29ca21cd
Some bugfixes for yesterday's sparse data population enhancements.
2011-07-01 10:53:07 -04:00
bf3cd1ee72
Merged bug fix from Stable into Unstable
2011-06-30 18:30:22 -04:00
4b17f34640
Fixes to the packaging system to work with the new directory structure.
...
Also added a few R scripts to the list of files to include in the resources
directory of the binary distribution, at Ryan's request.
2011-06-30 18:27:17 -04:00
91f8ab115d
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-06-30 18:15:53 -04:00
419bf259ee
Large number of bugfixes for bugs encountered while trying to scale up preQC database generation to all reprocessed data:
...
- Better support for missing data, esp. in eval files.
- More R-compatible date formatting.
- Some of the AlignmentSummaryMetrics were only for first of pair.
- Some of the InsertSizeMetrics retrieved data for only one pairing orientation.
- More/better command-line customization.
2011-06-30 18:03:59 -04:00
510efa3313
Merged bug fix from Stable into Unstable
2011-06-30 15:27:04 -04:00
5786b51bcf
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-30 15:26:28 -04:00
761347b8d5
The VariantContext utility method used by SelectVariants wasn't checking the filter status (unfiltered vs. passing filters) and always returned a VC that was passing filters. This is fixed and the md5 from the VCF Streaming test has been re-updated.
2011-06-30 15:26:09 -04:00
47b47078ad
Merged bug fix from Stable into Unstable
2011-06-30 15:22:14 -04:00
64048a67e8
cleaning up ghost scala scripts. Deleting clearly unused one and moving others to qscripts.archive
2011-06-30 15:20:43 -04:00
b17ed7e504
Merged bug fix from Stable into Unstable
2011-06-30 15:04:30 -04:00
867056af51
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-30 15:03:18 -04:00
57806d514a
Merged bug fix from Stable into Unstable
2011-06-30 15:01:50 -04:00
defa3cfe85
Moved around private walkers into appropriate directories in private gatk.walkers. Moved a few public walkers into private qc package, and some private qc walkers into the public directory. Removed several obviously broken and/or unused walkers.
2011-06-30 14:59:58 -04:00
75f93882c7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-30 14:59:10 -04:00
41c43d6248
Merged bug fix from Stable into Unstable
2011-06-30 14:56:42 -04:00
2cb1376ed0
VCFStreaming was failing integration tests because now select variants outputs the samples in alphabetical order, instead of random as before. Fixed the MD5.
2011-06-30 14:55:39 -04:00
f4ae6edb92
Moving some of the released R scripts into public from private
2011-06-30 14:55:25 -04:00
197b7141c1
Added an optional argument -bt <num_threads> for BWA to run multithreaded.
2011-06-30 14:41:57 -04:00
Ryan Poplin
Guillermo del Angel
Khalid Shakir
Eric Banks
David Roazen
Mauricio Carneiro
Matt Hanna
Mark A. DePristo