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4726 Commits (61875e4dfa4e2b6c251ccb264fbb03a0af0a7c35)

Author SHA1 Message Date
Ron Levine 61875e4dfa Fix LeftAlignAndTrimVariants -split to not change no-call genotypes to hom-ref 2017-02-22 17:57:59 -05:00
Ron Levine ab75b08ea7 Remove unused compressed_block_size and close BlockCompressedInputStream 2017-02-17 12:22:53 -05:00
Ron Levine 1d36d9fd69 Move htsjdk to ver 2.9.0 and picard to ver 2.8.3 2017-02-17 07:03:03 -05:00
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
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
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
Ron Levine 262c08aee3 Make exit system file type message generic 2016-11-23 10:12:21 -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 2d06f33227 Set HTSJDK log level 2016-11-15 07:08:19 -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
David Benjamin 029632eb1c backport numerics changes in new qual 2016-11-01 03:16:21 -04:00
Ron Levine d7090ef158 Write saved WARN messages to stderr instead of stdout 2016-10-21 13:01:07 -04:00
Ron Levine 0d2a3e754c Merge pull request #1490 from broadinstitute/rhl_ggvcf_hom_ref_high_mq 
Remove RankSumTest and RMSAnnotation from hom-ref sites
 2016-10-14 14:41:49 -04:00
Ron Levine 01a858542f Remove RankSumTest and RMSAnnotation from hom-ref sites 2016-10-14 11:34:54 -04:00
Ron Levine cfd3ffa2c0 Replace SAMFileReader with calls to SamReaderFactory 2016-10-14 11:22:54 -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 2c83081560 Remove sra group 2016-09-23 17:39:10 -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 ab454e8812 Upgrade Apache Commons Collections to version 3.2.2 2016-09-07 18:59:21 -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 abc4d5b7b3 Bypass spanning deletions in Rank Sum tests 2016-08-17 14:02:22 -04:00
Peter Fan 01fdb90096 Merge pull request #1452 from broadinstitute/pf_excludeIntervalPadding 
addresses issue #1280 now interval padding works for exclude intervals
 2016-08-17 13:15:15 -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
Peter Fan 3510906c7f addresses issue #1280 now interval padding works for exclude intervals 2016-08-10 13:45:45 -04:00
Andrii Nikitiuk a465c87ff8 Added support for directly reading SRA runs 2016-08-02 15:21:14 -04:00
Ron Levine 4f2e312805 Throw an exception for invalid Picard intervals 2016-07-15 11:20:53 -04:00
Laura Gauthier 641382eb8b Fix BetaTestingAnnotation group 
Add test
 2016-07-13 16:05:21 -04:00
Ron Levine aace73e884 Enable control of reporting periodicity 2016-07-13 07:24:03 -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
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
meganshand 556cc69185 Fix for int overflow in RankSum calculation 2016-06-29 12:02:13 -04:00
Valentin Ruano Rubio 07052ba8ea Changes to use the median rather than the second best likelihood for the NON_REF allele 
Addresses issue #1378 following the first proposal using the 'median' rather than the 'mean'.
 2016-06-28 13:10:22 -04:00
Ron Levine 3c5eac8c17 Move htsjdk and picard to version 2.5.0 2016-06-28 09:42:32 -04:00
sooheelee 6fe80d53d0 Improve documentation 
Clarified that this also filters supplementary alignments.
 2016-06-23 16:20:00 -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