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333 Commits (8c15d3ccd84810ac2ed5178e2e4fe6b372bfe202)

Author SHA1 Message Date
Ron Levine e5c5804141 Modify MD5s to correct RankSum annotations 2016-03-01 14:05:51 -05:00
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
Takuto Sato 243a0fcb74 Allele-specific insert size ranksum annotation 2016-01-28 16:03:57 -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
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
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
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 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 aa5e88a393 Fix exception when writing gVCF to stdout 2015-12-29 15:30:53 -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 9c8f035780 LeftAlignAndTrimVariants --splitMultiallelics keeps GT if valid 2015-12-14 10:42:32 -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
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 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
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
Geraldine Van der Auwera 1cf66addaa Deprecate tools that were outdated or redundant 
ReadAdaptorTrimmer (unsound and untested)
BaseCoverageDistribution (redundant with DiagnoseTargets)
CoveredByNSamplesSites (redundant with DiagnoseTargets)
FindCoveredIntervals (redundant with DiagnoseTargets)
VariantValidationAssessor (has a scary TODO -- REWRITE THIS TO WORK WITH VARIANT CONTEXT comment and zero tests)
LiftOverVariants, FilterLiftedVariants and liftOverVCF.pl (in #1106) (use Picard liftover tool)
sortByRef.pl (use Picard SortVCF)
ListAnnotations (useless)

Also deleted the java archive from the private repository (old junk we never use)
 2015-11-20 22:49:40 -05:00
meganshand 2570cab24c Assorted documentation fixes, enhancements and reorganization. 
See issues referenced by the pull request for details.
 2015-11-20 22:44:46 -05:00
Mark Fleharty 1443ee8c7f Fixes testPRWithConflictingArguments_qqAndSQQ to use -ql rather than -q1 2015-11-20 11:23:02 -05:00
Ron Levine ccaddefa19 Validate VCF with sequence dictionary 2015-11-20 09:23:24 -05:00
Yossi Farjoun 4da0d1300c adding fraction informative reads annotation. 2015-11-18 08:39:47 -05:00
David Roazen 9d5be24778 Move GatherBqsrReports from private to protected 2015-11-10 17:40:58 -05:00
Laura Gauthier 25b8ba45f4 More allele-specific annotations: AS_QD and AS_InbreedingCoeff 
Grouped default output annotations to keep them from getting dropped when -A is specified; addresses #918
Also refactored code shared by ExcessHet and InbreedingCoeff
 2015-11-09 16:38:31 -05:00
vruano e3d5d96076 Added the AF indepdent calculator for any ploidy but seems that is not doing a good job for haploid 
Addresses issue #1078 by implementing a any-ploidy version of the independent-allele-exact-ac-calculator already available for diploids.

Notice that this will change result somewhat when dealing with noisy data (low GQs).
 2015-11-07 16:17:30 -05:00
Mark Fleharty 8857bc9b3f Resolves issue #1061 to use testid1 rather than testid in two integrationtests. 2015-11-05 22:20:20 -05:00
Eric Banks 975f8a8502 Merge pull request #1206 from broadinstitute/eb_suppress_alt_allele_warnings 
Suppress emission of the scary warning message from genotyping to no …
 2015-11-05 16:12:50 -05:00
Eric Banks 2cc7de4886 Suppress emission of the scary warning message from genotyping to no more than once in 
anything but DEBUG logging mode.  Otherwise it fills up our output logs.
 2015-11-05 14:19:21 -05:00
meganshand e4627ed5c3 Addressing comments 2015-11-04 11:00:01 -05:00
meganshand b5165b8d30 Fix for out of date VCF version output 2015-11-03 17:35:47 -05:00
ldgauthier 3d1dc303b3 Merge pull request #1197 from broadinstitute/ts_ve_nullPointer 
Prevent null pointer exception in PrintMissingComp module
 2015-11-02 14:42:50 -05:00
Takuto Sato 33462c7b50 Removed the line that caused a null pointer, as the information it logged was not useful. Updated docs and added an integration test to ensure the code no longer throws the exception. 2015-11-02 12:45:09 -05:00
Laura Gauthier f7eb5d3082 Enable family-level stratification (if a ped file is provided) 2015-10-28 09:55:04 -04:00
Laura Gauthier 68a2f1243d Finished draft of code for new map-combine-reduce annotation framework 
All VQSR annotations can be generated in allele-specific mode
Pull out allele-specific annotations in AS_Standard annotation group
 2015-10-27 09:44:49 -04:00
Laura Gauthier fcaf37279c Finished draft of code for new map-combine-reduce annotation framework 
All VQSR annotations can be generated in allele-specific mode
Pull out allele-specific annotations in AS_Standard annotation group
 2015-10-27 09:23:29 -04:00
Ron Levine 36ca9fe898 Allow LeftAlignAndTrimVariants to handle alleles longer than the default processing window 2015-10-25 20:33:56 -04:00
Ron Levine 795fe75886 Update doc for multiallelics, trimming is the default behavior 2015-10-22 04:04:09 -04:00
Takuto Sato df7a482335 VariantAnnotator now supports annotating FILTER field from an external resource. 
Updated the docs.
 2015-10-14 14:26:21 -04:00
Ron Levine 2bcded11cb VariantAnnotator checks alleles when annotationg with external resource 2015-10-08 17:01:30 -04:00
Eric Banks 622ec352bb Fix for combining records in which one has a spanning deletion and needs a padded reference allele. 
This was erroring out and not working.
 2015-10-02 16:28:16 -04:00