zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
14,174 Commits
1 Branch
0 Tags
257 MiB
Commit Graph

14174 Commits (7896055be38b7cc38ab685760c1bd7b6ff3b3135)

Author SHA1 Message Date
Yossi Farjoun 7896055be3 - Fixed bug in GenomeLoc parser 
- Added a warning when two contigs are too similar that it might cause problems with parsing
- Added tests of modified parser and of warning.
 2016-02-02 06:53:22 -05:00
ldgauthier 8ab2eef6f0 Merge pull request #1282 from broadinstitute/ts_annotation 
Allele specific insert size ranks sum annotation
 2016-01-29 18:13:46 -05:00
Takuto Sato 243a0fcb74 Allele-specific insert size ranksum annotation 2016-01-28 16:03:57 -05:00
Geraldine Van der Auwera 1e4a98827c Merge pull request #1278 from broadinstitute/gvda-expose_queue_setting 
Expose time between checks as CLI argument (Queue)
 2016-01-28 11:00:36 -05:00
ldgauthier 0e969d9c5d Merge pull request #1279 from broadinstitute/ldg_removeExtraKBsamples 
Fix rogue false negatives from non-NA12878 samples in knowledgebase
 2016-01-28 08:32:20 -05:00
Laura Gauthier 633e729608 Reverted setupNA12878kb script to use old-style path names 
Import files are now derived from /humgen/gsa-hpprojects/NA12878Collection/knowledgeBase/runme.allLoci.csh, which subsets samples to NA12878 but maintains all loci
 2016-01-28 08:29:36 -05:00
ldgauthier ab5a8f0bb0 Merge pull request #1266 from broadinstitute/ldg_VQSRforAlleles 
Add new -AS mode to run VQSR (both VariantRecalibrator and ApplyRecal…
 2016-01-22 13:19:11 -05:00
Laura Gauthier 5592e4ead0 Add new -AS mode to run VQSR (both VariantRecalibrator and ApplyRecalibration) in an allele-specific manner 2016-01-22 13:18:21 -05:00
Geraldine Van der Auwera a46a4a6175 Expose time between checks for whether new jobs can be submitted as a user-settable parameter on CLi. Useful when testing pipelines to make idle time shorter. Contributed by @dakl (Daniel Klevebring on GATK forum). 2016-01-22 12:13:07 -05:00
Geraldine Van der Auwera 76817fe5ec Merge pull request #1276 from broadinstitute/gvda-remove_unneeded_dependency 
Remove unneeded dependency
 2016-01-21 16:51:34 -05:00
Geraldine Van der Auwera c93a611ea3 Remove unneeded dependency 
Addresses https://github.com/broadgsa/gatk/pull/15 for Guillermo
 2016-01-21 16:51:01 -05:00
Ron Levine 98eba7fb53 Merge pull request #1272 from broadinstitute/rhl_rm_variant_contig_order_check 
Remove variant contig order check
 2016-01-20 09:32:10 -05:00
Ron Levine ed933013fe Remove variant contig order check 2016-01-16 19:32:28 -05:00
Eric Banks c57c32b915 Merge pull request #1270 from broadinstitute/eb_small_genotyping_optimizations 
Small optimizations to the joint calling code.
 2016-01-13 08:46:57 -05:00
Eric Banks ab2f541d1f Small optimizations to the joint calling code. 
Thanks to profiling I noticed that the determineCoefficient() method was being called too often.
Because it returns a constant result in half of the invocations, its value should be cached when possible.
Also, the various calls to getLog10Likelihoods() showed up in the profiler, so I pulled those out too.

All told, it speeds up the genotyping by about 10 percent according to the profiler.
 2016-01-12 21:48:20 -05:00
ldgauthier d1565e4e6f Merge pull request #1261 from broadinstitute/ldg_VariantsToTableMultiallelicTypes 
Allow VariantsToTable to determine each allele's type when -SMA is used
 2016-01-12 10:47:22 -05:00
Laura Gauthier 593c9ddf01 Allow VariantsToTable to evaluate the type of each split variant when -F TYPE and -SMA are specified 2016-01-12 08:12:29 -05:00
Geraldine Van der Auwera 7f7ba446c0 Merge pull request #1269 from broadinstitute/dr_repair_3.5_tag 
Repair the 3.5 tag in unstable
 2016-01-08 16:06:33 -05:00
David Roazen dc5c08f940 Repair 3.5 tag in unstable by merging the missing 3.5 commit from stable 2016-01-08 15:33:15 -05:00
ldgauthier d9e0b7ba58 Merge pull request #1268 from broadinstitute/ldg_fixQueueTests3 
Remove "mem_free" from resident memory request params for Queue becau…
 2016-01-08 12:58:46 -05:00
Laura Gauthier 204cad3646 Remove "mem_free" from resident memory request params for Queue because it doesn't work and wouldn't actually reserve memory anyway 2016-01-08 10:27:56 -05:00
Ron Levine f002acebdf Merge pull request #1264 from broadinstitute/rhl_max_nocall_1262 
Backport maxNoCall functionality from GATK4
 2016-01-06 14:54:24 -05:00
Ron Levine d16ed98c9e Backport maxNoCall functionality from GATK4 2016-01-06 11:09:38 -05:00
ldgauthier 1d72ab099c Merge pull request #1247 from broadinstitute/ldg_VQSRmodelOutput 
Add optional argument for VQSR to output the model to a file as a GAT…
 2016-01-05 08:35:18 -05:00
Ron Levine 37746e40f4 Merge pull request #1263 from broadinstitute/rhl_rbp_not_merging_snps 
Merge consecutive SNPs on the same read
 2016-01-04 15:37:04 -05:00
Ron Levine fa1d90d236 Merge consecutive SNPs on the same read 2016-01-04 13:48:59 -05:00
Laura Gauthier 2ddc48914e Add optional argument for VQSR to output the model to a file as a GATKReport 
GATKReport output also has mean and variance for annotation normalization info
 2016-01-04 08:37:08 -05:00
ldgauthier 71c6709765 Merge pull request #1145 from broadinstitute/ldg_M2_HapMapSensitivity 
Fix no-normal bug; add HapMap sensitivity benchmarking
 2016-01-04 08:27:37 -05:00
Ron Levine 4b3b5636c6 Merge pull request #1265 from broadinstitute/rhl_hc_stdout_1259 
Fix exception when writing gVCF to stdout
 2015-12-29 23:07:53 -05:00
Ron Levine aa5e88a393 Fix exception when writing gVCF to stdout 2015-12-29 15:30:53 -05:00
meganshand 7089824e1b Merge pull request #1251 from broadinstitute/ms_annotations 
Adds new annotation, MQ of mate RankSum
 2015-12-23 12:36:43 -05:00
meganshand eb6bdb2a62 MQ of Mate RankSum annotation 
Intermediate commit for tests

Adding tests

Fixing tests after rebase

Fixing one MD5

Fixing documentation

Removing annotation from standard group

Adding documentation
 2015-12-23 10:24:40 -05:00
Laura Gauthier f9e9d2e273 Fix no-normal bug; add HapMap sensitivity benchmarking 2015-12-22 08:29:01 -05:00
Ron Levine 0c3c775566 Merge pull request #1248 from broadinstitute/rhl_keep_gt 
LeftAlignAndTrimVariants --splitMultiallelics keeps GT if valid
 2015-12-14 12:19:49 -05:00
Ron Levine 9c8f035780 LeftAlignAndTrimVariants --splitMultiallelics keeps GT if valid 2015-12-14 10:42:32 -05:00
Geraldine Van der Auwera 4767a83d8a Update pom versions to mark the start of GATK 3.6 development 2015-11-25 01:52:51 -05:00
Geraldine Van der Auwera e91472ddc7 Update pom versions for the 3.5 release 2015-11-25 01:29:48 -05:00
Geraldine Van der Auwera ee63b59b52 Merge remote-tracking branch 'unstable/master' 2015-11-25 01:27:41 -05:00
Geraldine Van der Auwera 9749adf22a Merge pull request #1236 from broadinstitute/gvda_prep_M2_release_1201 
Prep MuTect2 for release
 2015-11-24 20:12:57 -05:00
Geraldine Van der Auwera bf875974d1 Prep MuTect2 and ContEst for release 
Renamed M2 to MuTect2
    Renamed ContaminationWalker to ContEst
    Refactored related tests and usages (including in Queue scripts)
    Moved M2 and ContEst + accompanying classes from private to protected
    Made QSS a StandardSomaticAnnotation (new annotation group/interface) to prevent it from being sucked in with the rest of the StandardAnnotation group
 2015-11-24 16:43:20 -05:00
Geraldine Van der Auwera 1f8e45f0ba Merge pull request #1243 from broadinstitute/gvda_rodwalkers_dont_downsample_1179 
Fix bug where gatkdocs of RodWalkers reported default LocusWalker downsampling settings
 2015-11-23 21:39:43 -05:00
Geraldine Van der Auwera 88a0514ec7 Fix bug where gatkdocs of RodWalkers reported default LocusWalker downsampling settings 2015-11-23 17:53:19 -05:00
Mark Fleharty 5a3756410c Merge pull request #1231 from broadinstitute/mf_fixBQSRIntegrationTest 
Fixes testPRWithConflictingArguments_qqAndSQQ to use -ql rather than -q1
 2015-11-23 17:08:30 -05:00
Geraldine Van der Auwera b0730c2b81 Merge pull request #1239 from broadinstitute/gvda_straggler_doc_fixes_1237 
Improve doc block of GatherBqsrReports
Annotation doc enhancements (QD, InbreedingCoeff, ExcessHet and AS versions where applicable)
 2015-11-22 13:58:20 -05:00
Geraldine Van der Auwera 0babe6abf7 Merge pull request #1241 from broadinstitute/gvda_undeprecate_FindCoveredIntervals_1240 
Restore FindCoveredIntervals + add docs
 2015-11-22 13:56:25 -05:00
Geraldine Van der Auwera a7748368f8 Yet more doc improvements prior to 3.5 release 
Improve doc block of GatherBqsrReports
    Annotation doc enhancements (QD, InbreedingCoeff, ExcessHet and AS versions where applicable)
 2015-11-22 10:59:24 -05:00
Geraldine Van der Auwera 46ba0e519e Restore FindCoveredIntervals + add docs 2015-11-22 10:19:04 -05:00
Ron Levine 8f0ce02838 Merge pull request #1233 from broadinstitute/rhl_fix_example_bcf_dict 
Make the BAM header sequence dictionary match reference
 2015-11-21 21:45:16 -05:00
Ron Levine 08a9c80559 Make the header sequence dictionary match reference 2015-11-21 19:12:37 -05:00
Geraldine Van der Auwera 22fa1511be Merge pull request #1235 from broadinstitute/gvda_deprecate_useless_tools_1192 
Deprecate tools that were outdated or redundant
 2015-11-21 14:58:00 -05:00