81a4d18468
Mark several indel-related arguments as @Hidden
2011-07-06 09:56:38 -04:00
9124c84a7c
bug fixes
2011-07-04 21:10:44 -04:00
bb85f232b9
bug fixes
2011-07-04 21:04:49 -04:00
f26ffeaea0
bug fixes
2011-07-04 20:48:45 -04:00
04df153f47
bug fixes
2011-07-04 20:45:10 -04:00
7a04872a3f
bug fixes
2011-07-04 20:33:59 -04:00
08bc843d4c
SelectVariants can get a table to boost AF when choosing randomly
2011-07-04 20:23:22 -04:00
fac082de64
Report only highest AF and AC in multiallelic records in VariantsToTable or else R can't parse table
2011-07-03 14:32:12 -04:00
abe9480c6d
Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-02 21:19:15 -04:00
fb315b5f8c
Merge branch 'incoming'
2011-07-02 18:10:48 -04:00
41d46059e7
fixing bad format statement
2011-07-02 18:09:17 -04:00
3804afeb8a
Merge branch 'incoming'
2011-07-02 17:55:39 -04:00
781c0c33a4
Use the worst X% of calls in addition to the bad training sites list. Don't include the already added calls in the calculation of X%
2011-07-02 17:55:10 -04:00
6b8af6afd8
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-02 17:15:56 -04:00
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
4532a84314
Merged bug fix from Stable into Unstable
2011-07-02 10:48:55 -04:00
5faf40b79d
Moving AnalyzeAnnotations into the archive because it has outlived its usefulness.
2011-07-02 10:39:53 -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
c65e52f88a
Merged bug fix from Stable into Unstable
2011-07-01 20:50:56 -04:00
b6bc64a0c8
Cleanup of the utils.broad package.
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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
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
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
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
804d5f22d5
Reverting previous change, as promised.
2011-06-30 13:18:30 -04:00
9e234cf5d6
This is a temporary commit for Picard. It will absolutely break integration tests, but I'm going to revert it in 1 minute. Because we don't want them in unstable, I need to push this into stable.
2011-06-30 13:17:14 -04:00
331b47afbd
Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-06-30 08:29:11 -04:00
50c32ce52e
VariantsToTableFix
2011-06-29 21:39:53 -04:00
9b134f3b96
VariantsToTableFix
2011-06-29 21:33:41 -04:00
2b88033ef4
Enable considering 454 reads, just lower GOP by 15
2011-06-29 16:12:55 -04:00
dc4f63a1a8
a) consensus goes to week queue
...
b) New experimental TechnologyComposition annotation
c) SelectVariants fixes
2011-06-29 16:00:23 -04:00
70ba851478
Might as well check for the illegal state and throw an exception
2011-06-29 15:59:10 -04:00
1f19afe1d9
Fixed bug in the IndelRealigner: now that variants are correctly typed in VariantContext, it is possible that a variant can be an indel but neither an insertion or a deletion; added a isComplexIndel() method and now we check for such an event in the realigner (we don't use them to generate alternate consenses). Also, added a isMNP() method while I was there so that it would be consistent with other variant types.
2011-06-29 15:54:09 -04:00
e91ae6b265
AF matching when selecting random variants
2011-06-29 15:00:26 -04:00
dee10140dd
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-29 13:58:04 -04:00
8586c86bc4
My commit from last week to fix the old dbsnp rod conversion only worked for locus traversals. Updated now to work for all traversals.
2011-06-29 13:56:37 -04:00
5b6d279a2e
Two bug fixes:
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a) Modified the way clipped bases are dealt with in ReadPosRankSumTest when annotating indels. Cigar string cannot be trusted because BWA can clip good high quality bases and some sites get incorrect ReadPos annotations if BWA systematically clips at an indel breakpoint.
b) PL header needs to specify "." as length. Otherwise we fail VCF validation if multiallelic sites are present.
2011-06-29 10:21:27 -04:00
139c6b84a1
Modified build.xml and the help extractor doclet to use the output of "git
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describe" as an absolute version number (if the repository has at least one
tag), using the raw SHA-1 hash value as a fallback version number in the case
where there are no tags.
2011-06-28 08:37:05 -04:00
3c9497788e
Reorganized the codebase beneath top-level public and private directories,
...
removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.
2011-06-28 06:55:19 -04:00
Guillermo del Angel
Ryan Poplin
Khalid Shakir
Eric Banks
David Roazen
Mark A. DePristo