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283 Commits (2c94f74a95cbe2068c198e7c2dfcb44650c4ffa3)

Author SHA1 Message Date
Takuto Sato 2c94f74a95 Merge pull request #1404 from broadinstitute/ldg_M2_addM1filters 
MuTect 2: port strand artifact filter from MuTect 1
 2016-07-05 13:27:35 -04:00
Valentin Ruano Rubio 45607d1b30 RCM Variant sites merger won't output PL when there are too many alleles in order to avoid memory issues with large cohort runs. 
Small additional "cosmetic" changes to the code
Addresses issue #1419.
 2016-07-01 11:33:07 -04:00
Steve Huang 1ff234e7dd remove alt alleles, when genotype count is explosively large, based on alleles' highest supporting haplotype score; max tolerable genotype count is controlled by a default value overridable by user 
remove alt alleles, when genotype count is explosively large, based on alleles' highest supporting haplotype score; max tolerable genotype count is controlled by a default value overridable by user
 2016-06-30 22:36:49 -04:00
Takuto Sato 63e0865491 Built on Laura's code to port the strand bias filter from M1 and refactored code aroud SomaticGenotypingEngine. Added a new integration test. 2016-06-29 22:46:40 -04:00
Laura Gauthier 4066bcd75c Add new annotator for M1 clustered read position filter and M1 strand bias filter. 2016-06-29 22:46:37 -04:00
meganshand 1b921666a7 Change to max value of ExcessHet 2016-06-29 16:33:50 -04:00
Samuel Lee 76bb8fd9e5 Allows GatherBqsrReports to accept a .list file as input. 2016-06-22 12:39:18 -04:00
Ron Levine 427645162b SelectVariants works with non-diploids 2016-06-21 12:26:13 -04:00
Valentin Ruano Rubio 857459e420 Silly mistake '<' for a '<='. It was causing the exception when the exact number of alleles to drop was matching MAX_DROPPED_ALTERNATIVE_ALLELES_TO_LOG exactly (fixed to 20). 
I change the code to impose a maximum allele list message length instead and in the process I fixed the bug.
 2016-06-17 15:22:59 -04:00
Samuel Lee e119feee61 Added regression test for genotyping of spanning deletions in GenotypeGCVFs. 2016-06-15 09:48:26 -04:00
Geraldine Van der Auwera a76cb052e2 Ability to retry building VQSR model (contributed by mdp) 2016-05-31 18:57:55 -04:00
Geraldine Van der Auwera d87345cd1d GATKDocs overhaul 
- Fixed displaying of default values
    - Removed code cruft
    - Reorganized tooldoc categories and improved names
    - Reorganized tools within categories where applicable
    - Touched up various tool docs
    - Switched default gatkdocs output to html
    - Added parameter in agrregator pom to control output type
    - Set gatkdocs publishing script to output php
    - Deprecated GenotypeAndValidate walker
    - Added back PhoneHome arguments with @Deprecated annotations
 2016-05-29 16:35:08 -04:00
Geraldine Van der Auwera efbbbb1bd9 Add M2 to the HC annotations check 2016-05-27 13:49:31 -04:00
Geraldine Van der Auwera c4a06ad20a Move indel realignment to public 2016-05-27 12:39:58 -04:00
Valentin Ruano Rubio 9d32dec9cd Fix for the sum(AD) > DP bug. 
Closes issue #1340
 2016-05-26 15:04:52 -04:00
Steve Huang e1fadae139 Fix error in InfiniteRandomMatingPopulationModel.getLikelihoodsCalculator 
Same issue noticed in GATK4 [here](https://github.com/broadinstitute/gatk/issues/1856)
 2016-05-25 17:23:26 -04:00
Geraldine Van der Auwera 2c8356519c Merge pull request #1375 from broadinstitute/gvda_fix_offbyone_maxAltAlls_M2_#1297 
Fixed M2 max alt alleles threshold evaluation error
 2016-05-19 13:59:02 -04:00
samuelklee 7fdd3c2a0c Merge pull request #1358 from broadinstitute/sl_issue_1327 
Changed calls with GQ=0 to no-call for HaplotypeCaller in normal mode.
 2016-05-19 12:26:35 -04:00
Laura Gauthier 644076b1e1 Add fix and test for finalizing MQ annotation at BP resolution for variant and ref samples 
Addresses issue #1356
 2016-05-19 08:15:30 -04:00
Geraldine Van der Auwera f5456a3761 Fixed M2 max alt alleles threshold evaluation error 
Also clarified some argument docs
 2016-05-18 21:54:30 -04:00
Samuel Lee bf4b1a5421 Changed calls for GQ=0 from 0/0 to ./. for HaplotypeCaller in normal mode. 2016-05-18 13:17:27 -04:00
Ron Levine 35a06879f1 Move htsjdk and picard to version 2.3.0 2016-05-16 14:50:00 -04:00
David Benjamin 8623830267 Fixed bug in which consecutive SPAN_DELS were merged into a ** MNP.# 2016-05-06 01:36:14 -04:00
samuelklee aa0c76a166 Merge pull request #1326 from broadinstitute/sl_issue_1293 
Added maxNumPLValues argument to allow users to set maximum number of PL values in output.
 2016-04-28 10:52:27 -04:00
David Benjamin aecaa6d38e Allow GenotypeGVCFs to emit ref sites. 2016-04-27 15:53:44 -04:00
Geraldine Van der Auwera 14fe8b1e0e Moved BQSRGatherer and dependencies to the public module 2016-04-27 07:15:28 -04:00
Samuel Lee e08940a5a8 Added maxNumPLValues argument to allow users to set maximum number of PL values in output. 2016-04-26 23:30:25 -04:00
David Benjamin c040da427d Replace string literals for annotation groups. Closes #1216. 2016-04-19 15:54:44 -04:00
Laura Gauthier d573fc4adf Add some comments to AFCalculationResult 
Add note that VC may be null (in this case because there are too many alts)
Add todo for possible inefficient code
 2016-04-04 09:35:54 -04:00
Chris Norman 017828e4b7 Use the older murmur hash implementation that is included in the gatk jar. 2016-03-29 10:20:44 -04:00
Chris Norman c81795cf50 Fix license in DroppedReadsTracker. 2016-03-22 13:39:13 -04:00
Chris Norman a8ebf21ac3 Implementation of dropped read tracking. 2016-03-21 18:36:29 -04:00
Ron Levine b873467756 Merge pull request #1321 from broadinstitute/rhl_fix_hr_logger_name 
Change logger class to HomopolymerRun
 2016-03-16 11:44:40 -04:00
Ron Levine 5c0e97def4 Change logger class to HomopolymerRun 2016-03-16 10:01:21 -04:00
Laura Gauthier 9ffdfeccd5 Add test case for fix 2016-03-15 11:06:48 -04:00
Laura Gauthier 31fc64f82c To address weird case with all hom-refs, but alt allele is present, skip AS_QD for all-ref sites and remove raw annotations whether or not they can be successfully finalized 2016-03-15 09:34:47 -04:00
Ron Levine 6d7ec7377c Set --reference_window_stop if homopolymer is greater than window size 2016-03-14 18:09:41 -04:00
Geraldine Van der Auwera c81d5b898e Clarify VQSR inputs documentation 2016-03-11 16:38:33 -05:00
Geraldine Van der Auwera 4990ed706a Fixup for licensing update 2016-03-11 16:23:02 -05:00
ldgauthier d0432713e0 Merge pull request #1311 from broadinstitute/ldg_BetaTestAnnotationsGroup 
Add classes from "annotation party" to BetaTesting group
 2016-03-11 08:13:32 -05:00
Geraldine Van der Auwera 16ef36088e Merge pull request #1308 from broadinstitute/gvda_fix_license_quotes_#1307 
Update licenses
 2016-03-10 12:37:53 -05:00
Laura Gauthier 28cfb06513 Add AS_culprit and AS_VQSLOD to VCF header in ApplyRecalibration so output passes VCF validation 2016-03-09 08:22:58 -05:00
Laura Gauthier d9f9bd1d56 Add classes from "annotation party" to BetaTesting group 2016-03-09 08:17:44 -05:00
Geraldine Van der Auwera 9a306ca221 Update licenses 2016-03-05 01:09:43 -08:00
Geraldine Van der Auwera 2b70f14740 Misc documentation improvements 
Added caveat to VariantFiltration documentation
  Fixed PON creation example in M2 doc
  Improved MalformedReadFilter doc
  Updated N CIGAR error message
 2016-03-03 15:48:54 -08:00
Ron Levine 625941dc50 Merge pull request #1290 from broadinstitute/rhl_sac_nonref 
StrandAlleleCountsBySample selects most likely only from VCF alleles
 2016-02-29 17:05:57 -05:00
Ron Levine 5e2ffc188b Merge pull request #1295 from broadinstitute/rhl_sv_error_output_1194 
Correct error messages and error handling in multiple tools
 2016-02-29 17:05:24 -05:00
Ron Levine 40a5adf767 Change error output to use the correct argument 2016-02-29 13:21:03 -05:00
Ron Levine 80a22aad77 StrandAlleleCountsBySample selects most likely only from VCF alleles 2016-02-29 12:41:55 -05:00
meganshand c7e0f5b225 Removes Dithering from Rank Sum Test 
Fixing empty group case

Fixing MD5s

First comments addressed

Added permutation test

Adding new RankSum to AS_RankSum

Speeding up permutation algorithm and updating MD5s

Missed a few tests

Addressing comments

Changing md5s
 2016-02-29 11:45:27 -05:00