24e6da25ccMerge branch 'master' of ssh://gsa3/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2012-10-31 14:17:41 -0400
96344c6b62Add note to realigner docs
Eric Banks
2012-10-31 12:35:45 -0400
0a56fe5bc3Merge remote-tracking branch 'unstable/master'
Eric Banks
2012-10-31 12:17:24 -0400
651b1dbb97Merge branch 'unstable' into develop
Guillermo del Angel
2012-10-31 12:06:09 -0400
3dd290b142Merge branch 'develop' of github.com:broadinstitute/cmi-gatk into develop
Guillermo del Angel
2012-10-31 12:00:05 -0400
f5697532d6Added mvninstall.queue.all target which includes private, along with supporting sub-targets.
kshakir
2012-10-31 11:49:50 -0400
7dc0e26549Merge remote-tracking branch 'unstable/master' into unstable
Guillermo del Angel
2012-10-31 11:47:51 -0400
4580e99c0cMerge branch 'master' of ssh://gsa3/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2012-10-31 10:50:54 -0400
02b790c8dbMerge fix
Guillermo del Angel
2012-10-31 10:50:36 -0400
51a9ce28e1Merge remote-tracking branch 'unstable/master' into develop
Guillermo del Angel
2012-10-31 10:29:48 -0400
55ffbec000Fixes to set output QC files, prepare for GridEngine usage
Guillermo del Angel
2012-10-31 07:55:04 -0400
ec17bb1a75Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
Christopher Hartl
2012-10-30 16:52:14 -0400
eccb76c304Only run UG in the bundle for chr20
Eric Banks
2012-10-30 15:09:46 -0400
e1e480a0b9Bug fix: don't add no-call alleles to the list of ALT alleles being validated.
Eric Banks
2012-10-30 14:54:29 -0400
2aa28abe0aFixing md5s to reflect the new HapMap file
Eric Banks
2012-10-30 14:27:10 -0400
c8e17a7adftotally experimental UG feature, to be removed
Guillermo del Angel
2012-10-30 13:57:54 -0400
a3ba3e0a61fixed invocation of indel single sample VCF filter to supply GATK classpath
Kristian Cibulskis
2012-10-30 11:14:08 -0400
8a402024c2Updating bundle script to handle new naming convention of CEU trio best practices callset
Eric Banks
2012-10-30 09:11:56 -0400
c95e893920Better error message for unused ALT alleles
Eric Banks
2012-10-29 21:51:35 -0400
b6a1967f12Better documentation for ValidateVariants so that people realize it's used for strict validation of the VCF file. Added an option to turn off strict validation and an integration test to cover it.
Eric Banks
2012-10-29 21:47:09 -0400
21fa5f70caMerge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-10-29 18:53:41 -0400
5ee2feb2a3updating pipeline test md5s
Ryan Poplin
2012-10-29 18:53:27 -0400
be902375ac'Bug' fix: fix the error message from the vcf validator so people realize that the file fails strict validation but still adheres to the spec.
Eric Banks
2012-10-29 16:29:27 -0400
4e661847b2DelocalizedBaseRecalibrator becomes the BaseRecalibrator.
Ryan Poplin
2012-10-29 12:53:39 -0400
5070304ef4Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Menachem Fromer
2012-10-29 11:50:29 -0400
ac99437eecBug fixes to hapmap conversion in VariantsToVCF
Eric Banks
2012-10-29 01:45:33 -0400
43f7e8dc47Queue installed in aws refuses to see new GATK extension, so disable for now. Reenable QC now that Rscript is installed in cloud
Guillermo del Angel
2012-10-28 15:58:36 -0400
9fe79ec74bReenable parallelization in BQSR
Guillermo del Angel
2012-10-27 19:56:46 -0400
c21bc5ac4cHook up duplicate metrics to script outputs. Disable GC and multiple metrics until R is installed in nodes
Guillermo del Angel
2012-10-27 19:48:48 -0400
43625f652eShoot, mixed up the md5s last time.
Eric Banks
2012-10-27 19:43:46 -0400
f3ac5d404dupdating vcf header attribute descriptions in order to reflect correctly what's actually being written...
Andrey Sivachenko
2012-10-26 23:52:21 -0400
b4fbf6280afixing missing sample genotype bug, missing AD/DP bug, and putting annotations in more natural order (Ref/Alt)
Andrey Sivachenko
2012-10-26 23:48:40 -0400
ac5e58a265Bugfix for GSA-540 / Update metadata maps when adding lines to VCFHeader
Mark DePristo
2012-10-26 16:34:07 -0400
fa9b2a91d0Bugfix for GSA-552
Mark DePristo
2012-10-26 16:25:22 -0400
682a72faf7Hmm, thought I got all the md5s last time. Apparently not.
Eric Banks
2012-10-26 16:10:12 -0400
db8cbb5444Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
Christopher Hartl
2012-10-26 15:15:10 -0400
b0dcc2c78eMerge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-10-26 15:14:41 -0400
610e003b93Fixing a bug in the BQSR where the reference context gets out of sync after a read is adapter clipped inside the walker.
Ryan Poplin
2012-10-26 15:14:27 -0400
35483a7eefUpdate MD5s for PrintReads with BQSR Integration Test
David Roazen
2012-10-26 14:15:16 -0400
f66d812778Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-10-26 13:20:41 -0400
a8704ca73fAdding TODO notes for Ami
Eric Banks
2012-10-26 13:20:27 -0400
251983b8fbAdd GATK-wide command line argument to control the maximum runtime allowed for the GATK
Mark DePristo
2012-10-26 13:18:18 -0400
46099af8dbMerge branch 'master' of ssh://gsa2/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-10-26 12:10:53 -0400
ed11b7dab2Fix UG parallelization test
Eric Banks
2012-10-26 12:10:44 -0400
7a706ed345Fix some of the broken integration tests
Eric Banks
2012-10-26 11:23:44 -0400
27a4d6d90eMerge branch 'master' of ssh://gsa4/humgen/gsa-scr1/gsa-engineering/git/unstable
Yossi Farjoun
2012-10-26 09:33:10 -0400
a3193a1743fixed LargeScaleValidationCallingSingle.scala for new version of scala
Yossi Farjoun
2012-10-26 09:32:19 -0400
28393e9b30Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Menachem Fromer
2012-10-26 03:55:02 -0400
ebebec7fdbAccidentally left one test disabled
Eric Banks
2012-10-26 02:15:32 -0400
b06f689d4bMerge branch 'master' of ssh://gsa2/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-10-26 02:13:26 -0400
a53e03d525Do not let reduced reads get removed in the contamination down-sampling
Eric Banks
2012-10-26 02:13:04 -0400
9af4b34fd8Changed @Input to @Argument for non-File types
Menachem Fromer
2012-10-26 01:21:05 -0400
bf3d61ce82The default value for --contamination_fraction_to_filter is now 0.05 (5%) in both UG and HC. Users of GATK-lite get pushed down to 0% by default (since it's not enabled) or get a user error if they try to set it.
Eric Banks
2012-10-26 01:04:51 -0400
91f2c847a3Fixing problem reported on forum for VF: DP couldn't be filtered from the FORMAT field, only from the INFO field. Fixed and added integration test.
Eric Banks
2012-10-26 00:57:40 -0400
e0fa7d1497Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Menachem Fromer
2012-10-26 00:14:58 -0400
d879c77acaDon't scale up memory requirements by nct for PrintReads tests
Mark DePristo
2012-10-25 17:43:49 -0400
6b8b7df651Queue now understands -nct and requests the appropriate number of cores from LSF, SGE, etc
Mark DePristo
2012-10-25 17:26:29 -0400
422e16c62eBaseRecalibration: don't cache instances of ReadCovariates across reads
David Roazen
2012-10-25 16:16:00 -0400
92fa7e953aMerge branch 'master' of ssh://gsa3/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2012-10-25 16:33:14 -0400
0fe36b1c72Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Menachem Fromer
2012-10-25 16:18:57 -0400
cde4f037d3Begin moving XHMM scripts to public
Menachem Fromer
2012-10-25 16:18:25 -0400
dde3060bb8add the CEUtrio best practices results (UG + PBT) to the bundle
Ami Levy Moonshine
2012-10-25 15:36:17 -0400
90b9971033Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ami Levy Moonshine
2012-10-25 15:32:29 -0400
884d031e72NestedIntegerArray: Pre-allocate only the first two dimensions
David Roazen
2012-10-25 13:30:49 -0400
cc8c12b954Committing a broken version of BaseRecalibration
Mark DePristo
2012-10-25 14:46:09 -0400
e93ff3ea6eLet's go back to having the SB/SLOD NOT computed by default. If you recall, it was only enabled by default because we thought we were going to use it when we made VQSR use random forests. But since we decided not to change VQSR, there's no reason to triple the computation for every variant site anymore.
Eric Banks
2012-10-25 12:45:23 -0400
69f2f1ef29Merge fix
Guillermo del Angel
2012-10-25 12:08:49 -0400
2e8366d2d8Bug fixes in setting @outputs, fix to make IndelRealigner scatter-gather correctly
Guillermo del Angel
2012-10-25 12:07:35 -0400
a838653822Merge branch 'master' of ssh://gsa3/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2012-10-25 10:35:58 -0400
596c1723aeHidden, unsupported ability of VariantEval to run AlleleCount stratification on sites-only VCFs. I'll expose it/add tests on it if people think this is generaly useful. User needs to specify total # of samples as command line argument since genotypes are not available. Also, fixes to large-scale validation script: lower -minIndelFrac threshold or else we'll kill most indels since default 0.25 is too high for pools, fix also VE stratifications and add one VE run where eval=1KG, comp=pool data and AC stratification based on 1KG annotation
Guillermo del Angel
2012-10-25 10:35:43 -0400
6dc7d872ecFix GenotypeAndValidate to handle SNPs and indels as reported on the forum. Recent changes to the UnifiedArgumentCollection made this stop working. Adding in JIRA to create integration tests for this tool.
Eric Banks
2012-10-25 10:06:13 -0400
c53c55da12Re-enable tests
Eric Banks
2012-10-25 09:37:08 -0400
e6652f7777Added integration test for contamination down-sampling
Eric Banks
2012-10-25 09:36:05 -0400
3db9703a65Merge branch 'develop' of github.com:broadinstitute/cmi-gatk into develop
Kristian Cibulskis
2012-10-25 09:21:08 -0400
1788e596c7DEV-14 #resolve #time 3m
Kristian Cibulskis
2012-10-25 09:20:48 -0400
df9e0b7045Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-10-25 02:49:54 -0400
72714ee43eMinor patches to get the contamination down-sampling working for indels. Adding @Hidden logging output for easy debugging.
Eric Banks
2012-10-25 02:47:42 -0400
c6b57fffdaAdded allele biased down-sampling capabilities to the PerReadAlleleLikelihoodMap object, which means that both the UG and HC can use this functionality. Note that it's only available in protected, so GATK-lite users won't be allowed to enable it. Needs more testing.
Eric Banks
2012-10-24 22:52:25 -0400
327d6f98d7fixed duplicate argument names
Scott Frazer
2012-10-24 22:18:18 -0400
bcf3582095Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ami Levy Moonshine
2012-10-24 21:50:41 -0400
660fc120a3QC fixes in fastq-bam: a) Connect picard outputs with @Output b) Do QC by default and correct picard path in instances. c) EXPERIMENTAL: bump up numThreads to 8 by default and see what happens DEV-155 #resolve #time 1m
Guillermo del Angel
2012-10-24 21:37:25 -0400
2d9e2e6b8eDelete ExperimentalNestedIntegerArray
David Roazen
2012-10-24 19:59:46 -0400
9da7bbf689Refactoring the PerReadAlleleLikelihoodMap in preparation for adding contntamination downsampling into protected only.
Eric Banks
2012-10-24 15:49:07 -0400
d9aa9855f8Better comments in NestedIntegerArray
David Roazen
2012-10-24 15:29:13 -0400
02018ca764Legacy BaseRecalibrator walker is neither TreeReducible nor NanoSchedulable
David Roazen
2012-10-24 15:06:13 -0400
32a6d7000aThread-safe ReadGroupCovariate
David Roazen
2012-10-24 13:06:34 -0400
991658acf4BQSR: use more granular locking for concurrency control
David Roazen
2012-10-22 13:36:07 -0400
a27ee26481updating HC integration test.
Ryan Poplin
2012-10-24 14:08:39 -0400
094db7bf24We now require at least 10 samples to merge variants into complex events in the HC. Added a new population based bam for the complex event integration test.
Ryan Poplin
2012-10-24 14:07:36 -0400
5b7b42356bFix bug in GenotypeAndValidate where it doesn't check vc.hasAttribute() before using vc.getAttribute().
Eric Banks
2012-10-24 14:02:50 -0400
53ab02d1fcAdded @Input and @Output indexes for bam/vcf.
kshakir
2012-10-24 11:24:46 -0400
6e421a72d6Add more exhaustive unit tests for input errors to NanoScheduler
Mark DePristo
2012-10-23 20:10:39 -0400
8dfa24df7bSending a version of per job status messages. In addition to outputs, inputs are passed to QStatusMessenger.done() CloneFunction.cloneIndex has a new CloneFunction.cloneCount companion useful for display purposes.
kshakir
2012-10-23 12:34:26 -0400
5fac5bf12eFixed issues with Queue packaging of Picard QC classes: separate jar's are needed fromPicard. User needs to specify the -picardBase argument to point to input path for jars. > Also, reenable joint cleaning as now it works. > DEV-125 #resolve > DEV-90 #resolve
Guillermo del Angel
2012-10-23 14:08:31 -0400
Guillermo del Angel
Eric Banks
kshakir
Christopher Hartl
Kristian Cibulskis
Ryan Poplin
Menachem Fromer
Mauricio Carneiro
Andrey Sivachenko
Mark DePristo
David Roazen
Yossi Farjoun
Ami Levy Moonshine
Scott Frazer