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1540 Commits (dca24a9fa4391084076f0febbdf92af083b5cb09)

Author SHA1 Message Date
Ron Levine 5602095a24 Move htsjdk to ver 2.8.1 and picard to ver 2.7.2 
- Updating VF and tests to match new jexl behavior from htsjdk
     - Use Z instead of DP to test behavior on missing annotation
 2016-12-10 11:50:30 -05:00
meganshand 1291cfa881 Merge pull request #1529 from broadinstitute/ms_fs 
Make Fisher Exact Test match R and GATK4 p-values
 2016-12-06 08:55:08 -05:00
Ron Levine 172db666d6 Output files with the vcf.gz extension are gzipped, containing .bcf not as an extension result in VCF" 2016-12-05 22:25:59 -05:00
Geraldine Van der Auwera 234ccdf0c3 Merge pull request #1496 from broadinstitute/db_m2_downsampling 
Expose downsampling parameters as CLI arguments to Mutect2
 2016-12-05 21:53:25 -05:00
meganshand 3265a664c4 Makes Fisher's exact test match R and GATK4 2016-12-05 16:46:47 -05:00
David Benjamin b1f2301dd3 Add downsampling arguments to Mutect 
- maxReadsInRegionPErSample, minReadsPerAlignment start are now M2 args
	- maxReadsInMemoryPerSample is an activeRegionWalker arg
 2016-12-05 14:12:22 -05:00
Geraldine Van der Auwera b42dc1624b Documentation fixes 
- Fix missing closing code block tag
	- SOR fix + minor fix to template
	- Minor typo fixes
	- Make no_cmdline_in_header arg visible in docs
	- Caveats for UG-only args that are difficult to move out of common collection
	- Reference -L and -XL in -gvcf documentation
	- Annotation doc fixes (dsde-docs#1289)
	- Unhide some ContEst args and make Advanced
	- Fix inputPrior error message
	- Update web urls
	- Add JEXL doc link
 2016-12-05 14:09:44 -05:00
Ron Levine 68b6f8f638 Replace VariantContextWriterFactory with VariantContextWriterBuilder 2016-11-30 16:04:25 -05:00
David Benjamin 055d653bc2 Merge pull request #1517 from broadinstitute/rhl_adapter_boundary_err_1406 
Fix adapter bounday for positive strand
 2016-11-18 10:25:46 -05:00
Ron Levine 22d94a7096 Fix adapter bounday for positive strand 2016-11-16 16:41:17 -05:00
David Benjamin 6156b85ad9 Fixed logic error and tidied AlleleBalance and AlleleBalanceBySample 2016-11-16 14:10:48 -05:00
Ron Levine d61b4c7e91 Change the truth VCF 2016-11-15 14:56:15 -05:00
Geraldine Van der Auwera 2b83dd7c5b Added TreeReduce interface to VariantFiltration 2016-11-14 17:19:44 -05:00
Ron Levine bcbd7fe952 Change default value of STANDARD_CONFIDENCE_FOR_CALLING to 10 2016-11-11 02:06:41 -05:00
Ron Levine df0ba2ce8d BaseCountsBySample counting bases at a particular position 2016-11-08 13:31:05 -05:00
David Benjamin 029632eb1c backport numerics changes in new qual 2016-11-01 03:16:21 -04:00
Steve Huang cc91052e69 fixed a max priority Q error while removing alt alleles when faced with high ploidy and allele count; added hackish integration test (#1457) 2016-10-27 11:19:49 -04:00
Ron Levine 01a858542f Remove RankSumTest and RMSAnnotation from hom-ref sites 2016-10-14 11:34:54 -04:00
Valentin Ruano Rubio 16417bbf34 Fixes NaN issue in new Qual calculator 
Fixes issue #1491
 2016-10-11 16:03:06 -04:00
Ron Levine 81a9ece45b deprecate -stand_emit_conf 2016-10-09 10:24:09 -04:00
Ron Levine 4ef396f72e Assign correct ambiguity code for * allele 2016-09-22 11:02:44 -04:00
David Benjamin 318bee2269 Backport new AFCalculator 2016-09-21 15:21:56 -04:00
Ron Levine c13e3752d6 Move htsjdk to ver 2.6.1 and picard to ver 2.6.0 2016-09-16 16:36:52 -04:00
Ron Levine 6564066de3 Remove NON_REF from allSites VCF output 2016-09-16 13:55:52 -04:00
Steve Huang 091d05370b Fix 1448 to make alt allele removal by likelihoods robust to ref allele indices (#1475) 
* alt alle removal by likelihoods now robust to ref allele indices (no longer assumes 0-indexed ref)
 2016-09-13 21:20:44 -04:00
Ron Levine a7b1130224 Do not emit GVCF block definitions in the header 2016-09-09 07:41:03 -04:00
Ron Levine 956b18fbb7 Make ReadPosRankSumTest.isUsableRead() account for deletions 2016-09-07 13:52:09 -04:00
Steve Huang 3c88e6859f fix 1430 for genotype filters; refactored filter() method; added unit and integration test; more comprehensive fix must be done first on htsjdk side in JEXLMap (#1456) 2016-09-06 17:30:18 -04:00
David Benjamin 601c26a592 More small refactorings of Mutect2 code 2016-08-29 12:45:13 -04:00
Ron Levine a883905101 Remove -stand_emit_conf argument 2016-08-26 22:09:11 -04:00
Takuto Sato bc3b3ac0ec Cleaned up SomaticGenotypingEngine::callMutations and added some TODOs. 2016-08-26 14:12:05 -04:00
David Benjamin 4aede99697 Merge pull request #1453 from broadinstitute/db_mutect2 
Lots of small improvements to Mutect2 code
 2016-08-23 18:35:38 -04:00
Ron Levine cd5c04f806 Make getElementForRead() in RankSumTest robust 2016-08-23 14:56:32 -04:00
David Benjamin 01142dfb1c Lots of small improvements to Mutect2 code 2016-08-23 09:50:48 -04:00
Ron Levine abc4d5b7b3 Bypass spanning deletions in Rank Sum tests 2016-08-17 14:02:22 -04:00
Peter Fan 3510906c7f addresses issue #1280 now interval padding works for exclude intervals 2016-08-10 13:45:45 -04:00
Samuel Lee 49507faaa3 Changed maximum allowed GQB value to 100. 2016-08-05 13:06:31 -04:00
Andrii Nikitiuk a465c87ff8 Added support for directly reading SRA runs 2016-08-02 15:21:14 -04:00
Samuel Lee 832a383acd Fixed MD5 broken by PR #1440. 2016-07-27 13:51:20 -04:00
samuelklee 9a6ce7a347 Merge pull request #1440 from broadinstitute/sl_issue_1345 
Added exception for GQB values greater than MAX_GENOTYPE_QUAL and tests.
 2016-07-26 14:55:59 -04:00
Valentin Ruano Rubio fef63ce6a8 Make sure that multi-alleleic uninformative PLs (0,0,...,0) stay uninformative after biallelization. 
Addresses issue #1439 (thus #1437).

Fixes a bug where non informative PLs were not handled appropriatelly when calculating multi-allelic site QUAL values.
This was resulting in long execution times for very large datasets (~200,000 samples in the case of ExAC2).
 2016-07-25 17:19:03 -04:00
Samuel Lee 3daed9e5a1 Added exception for GQB values greater than MAX_GENOTYPE_QUAL and tests. 2016-07-20 16:48:59 -04:00
Ron Levine 7392c4d1b0 Removed spanning deletions if the deletion was removed 2016-07-19 12:23:49 -04:00
Laura Gauthier 641382eb8b Fix BetaTestingAnnotation group 
Add test
 2016-07-13 16:05:21 -04:00
Takuto Sato d6d0678b50 Build on Laura's code and finish porting MuTect1 clustered read position filter. 2016-07-11 17:33:08 -04:00
Samuel Lee 9b32cf5291 Fixed merging of GVCF blocks by fixing rounding of GQ values in ReferenceConfidenceModel. 2016-07-06 10:08:08 -04:00
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