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Author SHA1 Message Date
Ernesto Brau e8b42c4dfd Use GKL's implementation of Vector Logless Pair HMM 
Fixed MuTect2 tests by removing old -alwaysloadVectorHmm flag; upgraded to GKL 0.5.2; FASTEST_AVAILABLE pairhmm option; improved documenting comments in code

Made FASTEST_AVAIALABLE the default for the pairHMM cmdline argument

Make LOGLESS_CACHING the default pairHMM unified cmdline argument, fix error message if choose an unrecognized pairHMM

Updae MD5s
 2017-06-07 13:33:32 -04:00
Laura Gauthier 35d0b72c79 Changed calculation of rank sum so it's now the median of the per-sample rank sums (because the rank sum across all sample data did worse for biallelics). Now only called alt for 0/1s has rank sum, similar to old paradigm. Combined gVCF rank sums stored in Histogram, then median is taken once during genotyping. Histogram uses Integer keys to eliminate numerical precision mess 2017-05-10 09:04:42 -04:00
skwalker 4fe4ace232 minor bug fix in depth of coverage for partitioning by library + test (#1574) 
minor bug fix in depth of coverage for partitioning by library
 2017-04-26 10:42:54 -04:00
Ron Levine 278985b8bd Update PLINK link and change lines to columns 2017-03-23 11:46:38 -04:00
Ron Levine 4188745074 Document how VTT orders samples in output table 2017-03-21 18:04:38 -04:00
Geraldine Van der Auwera e86da63d04 Update pom versions to mark the start of GATK 3.8 development 2016-12-12 08:53:23 -05:00
Geraldine Van der Auwera 56f2c1ac75 Update pom versions for the 3.7 release 2016-12-12 08:49:43 -05:00
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
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
Geraldine Van der Auwera 2b83dd7c5b Added TreeReduce interface to VariantFiltration 2016-11-14 17:19:44 -05:00
Ron Levine df0ba2ce8d BaseCountsBySample counting bases at a particular position 2016-11-08 13:31:05 -05:00
Ron Levine 01a858542f Remove RankSumTest and RMSAnnotation from hom-ref sites 2016-10-14 11:34:54 -04:00
Pierre Lindenbaum a301ba1977 Add read group identifier to column names 
If two SAMReadGroupRecords share the same sample name, the output will contain duplicate column headers.
This PR fix the problem.
 2016-10-11 18:37:11 -04:00
Ron Levine 4ef396f72e Assign correct ambiguity code for * allele 2016-09-22 11:02:44 -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
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
Ron Levine f6c18a5182 Throw an exception if the BQSR input covariants file is not found 2016-08-11 12:46:14 -04:00
Andrii Nikitiuk a465c87ff8 Added support for directly reading SRA runs 2016-08-02 15:21:14 -04:00
Laura Gauthier 641382eb8b Fix BetaTestingAnnotation group 
Add test
 2016-07-13 16:05:21 -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
Ron Levine 3c5eac8c17 Move htsjdk and picard to version 2.5.0 2016-06-28 09:42:32 -04:00
Ron Levine c6ef81b611 Change HashMap to LinkedHashMap for predictable ordering 2016-06-23 10:48:22 -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
Yossi Farjoun f0f482c1fe - added an option to merge GenomeLocs that are abutting (contiguous) rather than actually overlapping. (#1399) 
- this should make ValidateVariants much faster.

- fixed NPE that occurs when there is no -L argument
 2016-06-06 11:46:15 -04:00
Geraldine Van der Auwera 85dce75f3f Update pom versions to mark the start of GATK 3.7 development 2016-06-01 17:21:48 -04:00
Geraldine Van der Auwera f185a75e1c Update pom versions for the 3.6 release 2016-06-01 17:08:17 -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 3cc7d7e56d Hide deletion arguments in ASEReadCounter 2016-05-27 12:46:13 -04:00
Geraldine Van der Auwera 81d4eaea29 Fixed warnings in LAATV and ValidateVariants 2016-05-27 12:46:02 -04:00
Geraldine Van der Auwera c4a06ad20a Move indel realignment to public 2016-05-27 12:39:58 -04:00
Yossi Farjoun 25fa25b618 Added option to validate gvcf (for ValidateVariants) (#1379) 
* with option --gvcf CLP will now put extra checks that a gvcf must adhere to (existance of <NON_REF> allele at every variant, and that the variants in total cover the entire requested intervals, or the whole genome if no intervals have been specified)
* works on gvcf produced by HC when using either GVCF or BP_RESOLUTION mode
* added positive and negative tests
 2016-05-26 06:42:45 -04:00
Geraldine Van der Auwera 6d5b643a9d Fix tagging syntax 
Syntax was given as -V:format,name but should be -V:name,format
 2016-05-17 08:42:49 -04:00
Ron Levine 35a06879f1 Move htsjdk and picard to version 2.3.0 2016-05-16 14:50:00 -04:00
Ron Levine f337b45724 Move htsjdk and picard to version 2.0.0 
Conflicts:
	protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java
	protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java
	protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
	protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
 2016-04-25 14:51:25 -04:00
Geraldine Van der Auwera 662919e5fe Correction to AlleleBalance doc 
Addresses https://github.com/broadinstitute/dsde-docs/issues/818

    The equations representing the allele balance calculation were confusing and inconsistent with both the description text and the code. This doc change brings consistency and correctness.

    Also improves the AB by sample doc accordingly.
 2016-04-25 12:10:01 -04:00
David Benjamin f639564599 Fixed bug in which PrintReads left out @PG header record 2016-04-22 08:46:18 -04:00
David Benjamin cfbf062f29 fixed bug in dbSNP binding in VariantAnnotationEngine 2016-04-21 14:38:31 -04:00
Ron Levine e2828104b1 SelectVariants and VariantFiltration not updating AC, AN and AF for --setFilteredGtToNocall 2016-04-17 10:24:05 -04:00
Ron Levine e4003bc792 Add informative exceptions to getSAMFileSamples() 2016-03-31 13:41:11 -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
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 d9f9bd1d56 Add classes from "annotation party" to BetaTesting group 2016-03-09 08:17:44 -05:00
Ron Levine 244a217ee7 Fix sample_gene_summary reports header order 2016-03-08 22:21:51 -05:00