bb79d3edae
Added GATKDocs for the BQSR walkers.
2011-08-18 10:57:48 -04:00
de35bb2e4d
Update hard-coded path of CNV read-depth merging script. The design of this pipeline needs to be corrected in the next few months...
2011-08-18 00:10:12 -04:00
c91a442be1
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 22:40:16 -04:00
b75a1807e3
Adding integration test to cover sample exclusion
2011-08-17 22:40:09 -04:00
a7b70e6bb4
Adding feature for Khalid: ability to exclude particular samples.
2011-08-17 22:28:22 -04:00
cc3df8f11a
Moving GAV walker to public
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Walker is updated to the new RodBinding system and has the new GATKDocs layout.
2011-08-17 21:55:17 -04:00
a9df365364
GenotypeAndValidate walker updated
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Updated the walker to comply with the new RodBinding system and the new GATKDocs. Will move it to public after writing integration tests.
2011-08-17 21:55:17 -04:00
fa1db3913b
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 21:49:25 -04:00
8e83b6646b
Bug fix for Chris: don't validate ref base for complex events.
2011-08-17 21:49:14 -04:00
2bbf29b07a
Merged bug fix from Stable into Unstable
2011-08-17 17:01:36 -04:00
c104dd7a09
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 16:59:12 -04:00
81a792afeb
Reverting optimization disable in unstable.
2011-08-17 16:58:24 -04:00
c193f52e5d
Fixed up examples: pasting from wiki still had old rod syntax
2011-08-17 16:29:45 -04:00
2b2a4e0795
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/stable
2011-08-17 16:26:45 -04:00
297c9e513c
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable into unstable
2011-08-17 16:24:02 -04:00
a210a62ab9
Merged bug fix from Stable into Unstable
2011-08-17 16:23:31 -04:00
fdd46a5e99
License automatically added.
2011-08-17 16:22:37 -04:00
d59e6ed274
Fix for RefSeqCodec bug and better error messages
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-- RefSeqCodec bug: getFeatureClass() returned RefSeqCodec.class, not RefSeqFeature.class. Really should change this in Tribble to require Class<T extends Feature> to get compile time type checking
-- Better error messages that actually list the available tribble types, when there's a type error
2011-08-17 16:22:07 -04:00
d170187896
Disable optimization that increases marginal speed of the GATK slightly but
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can produce data loss in a narrow corner case where the BGZF block(s) locations
and offsets in the last index bucket of contig n overlap exactly with the BGZF
block locations and offset in the last index bucket of contig n+1.
A proper fix that keeps the optimization has already been introduced into
unstable, but disabling the optimization is a low risk way to make sure that
users of stable experience no data loss.
2011-08-17 16:16:05 -04:00
53006da9a5
Improved descriptions for the SnpEff annotations in the VCF header
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(based on Eric's feedback).
2011-08-17 16:09:10 -04:00
784fb148b9
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 15:47:01 -04:00
671330950d
Updated Beagle walker for gatkdocs format. Pushed unsupported, undocumented arguments to @Hidden
2011-08-17 15:46:31 -04:00
0af68e052a
Merge branch 'master' of ssh://cga1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 15:17:47 -04:00
a423546cdd
fix: RefSeq contains records with zero coding length and the refsec codec/feature used to crash on those; now such records are ignored, with warning printed (once)
2011-08-17 15:17:31 -04:00
710d34633e
now the reads that are too long are truly ignored (fix of the fix)
2011-08-17 15:16:23 -04:00
40f64a27be
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 14:21:55 -04:00
2f19046f0c
Adding docs to the 2 beasts. Saved the worst for last.
2011-08-17 14:19:14 -04:00
8a92143938
Change @argument to @input
2011-08-17 14:18:34 -04:00
4dab59bfb5
Added: a simulator for intron loss reads.
2011-08-17 14:14:31 -04:00
eea8087c73
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 14:06:25 -04:00
069554efe5
somatic indel detector does not die on reads that are too long (likely contain a huge deletion) anymore; instead print a warning and ignore the read
2011-08-17 14:05:19 -04:00
c405a75f54
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 13:28:25 -04:00
575303ae6b
Renaming for consistency and bringing up to speed with new rod system
2011-08-17 13:28:19 -04:00
6d629c176c
Adding docs
2011-08-17 13:27:36 -04:00
a21e193a9e
Adding docs to 3 more walkers
2011-08-17 12:35:08 -04:00
98acb546a9
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 12:22:29 -04:00
d1bb302d12
Added GatkDocs documentation
2011-08-17 12:21:37 -04:00
3da71a9bb6
Clean up summary
2011-08-17 12:04:45 -04:00
c6fb215faf
GATKDocs for VariantsToTable
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-- Made a previously required argument optional, as this was a long-standing bug
2011-08-17 12:02:41 -04:00
5f794d16a7
Fixed bad character in documentation
2011-08-17 12:01:08 -04:00
9d1d5bd27a
Revert "Fixed bad character in documentation"
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This reverts commit a1f50c82d3cb25e5e83d36e9054d74cdee957d87.
2011-08-17 11:57:31 -04:00
78deb3f195
Fixed bad character in documentation
2011-08-17 11:57:00 -04:00
79dcfca25f
Fixed bad character in documentation
2011-08-17 11:56:51 -04:00
c365da3c51
Fixed final old rodBinding from PipelineTest
2011-08-17 11:56:30 -04:00
b3b5d608ca
Adding docs to yet more walkers
2011-08-17 09:57:19 -04:00
fadcbf68fd
Adding docs to QC walkers
2011-08-17 09:39:33 -04:00
5f3f46aad1
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-16 16:26:33 -04:00
946f5c53fe
Adding docs to more walkers
2011-08-16 16:26:26 -04:00
6e828260a0
Removed -B support. Now explodes with error if -B provided.
2011-08-16 16:13:47 -04:00
0c3466d2c3
typo
2011-08-16 15:25:35 -04:00
Ryan Poplin
Menachem Fromer
Eric Banks
Mauricio Carneiro
Matt Hanna
Guillermo del Angel
Mark DePristo
David Roazen
Andrey Sivachenko
Chris Hartl