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1421 Commits (7f7ba446c052cf5e4b560c663f9b028a1fd2f51d)

Author SHA1 Message Date
Laura Gauthier 204cad3646 Remove "mem_free" from resident memory request params for Queue because it doesn't work and wouldn't actually reserve memory anyway 2016-01-08 10:27:56 -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 4767a83d8a Update pom versions to mark the start of GATK 3.6 development 2015-11-25 01:52:51 -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
Kate Noblett 506958a0b7 Implemented a new VariantEval evaulation module, MetricsCollection. Fixed null pointer exception, updated tests. 2015-09-30 17:21:30 -04:00
Ron Levine 792142ec50 Implement BaseCounts per-sample 2015-09-30 08:59:11 -04:00
Samuel Lee c7f76b945e addressing PR comments 2015-09-24 15:42:51 -04:00
Samuel Lee 0dacf60012 Changed calls for RGQ=0 from 0/0 to ./. in output of GenotypeGVCFs. 2015-09-23 15:35:09 -04:00
Ron Levine 3ecabf7e45 Allow overriding ValidateVariants' hard-coded cutoff for allele length 2015-09-17 10:49:14 -04:00
meganshand 2507bf8d17 Fixed 7-PL genotypes in InbreedingCoeff tests 2015-09-14 12:00:45 -04:00
meganshand d767e1722e Excess Het P-value 
Added input exception

Added header line

Updated MD5s

Changing more MD5s

Made edge case clearer

Fixed formatting

Changed mid-point to mode
 2015-09-14 12:00:44 -04:00
Laura Gauthier 53b506a0b8 Make sure inputPriors get used if they are specified 
Fix usage of AF prior (i.e. theta) in probability of non-reference calculation
Refactored duplicate functions
Updated docs for heterozygosity
 2015-09-10 10:08:03 -04:00
Ron Levine 83a7012d69 Mask snps with --snpmask 2015-09-09 16:20:48 -04:00
Eric Banks b0dea2ccca Merge pull request #1150 from broadinstitute/eb_keep_iupac_in_IR 
Don't have the Indel Realigner change IUPAC reference bases.
 2015-09-04 13:43:34 -04:00