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228 Commits (37746e40f4c59e57bf01f622240d054ae0b5e544)

Author SHA1 Message Date
Ron Levine fa1d90d236 Merge consecutive SNPs on the same read 2016-01-04 13:48:59 -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
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
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Deprecate tools that were outdated or redundant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Geraldine Van der Auwera 1cf66addaa Deprecate tools that were outdated or redundant 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
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
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
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 792142ec50 Implement BaseCounts per-sample 2015-09-30 08:59:11 -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
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
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
Eric Banks 5f76ae6a37 Don't have the Indel Realigner change IUPAC reference bases. 
This change doesn't affect the performance of the Indel Realigner at all (as per tests).
This is just a request from the Picard side (where further testing is happening).
 2015-09-04 13:42:23 -04:00
ldgauthier cad81a6181 Merge pull request #1149 from broadinstitute/ldg_fixCGPbugForAndrea 
Fix bug when using --ignoreInputSamples
 2015-09-04 11:17:15 -04:00
Ron Levine 29ac64f6ce Calculate GenotypeAnnotations before InfoFieldAnnotations 2015-09-03 09:22:46 -04:00
Laura Gauthier 4769ef8dad Fix bug when using --ignoreInputSamples 2015-09-02 09:27:06 -04:00
Samuel Lee 41256e1405 Added file-extension--dependent interval-list output to RealignerTargetCreator. 2015-08-31 11:22:18 -04:00
Mark Fleharty daeb55429e Adding Static Binning to BQSR 2015-08-24 13:36:17 -04:00
Ron Levine 2afe3f7a21 Make GenotypeGVCFs subset Strand Allele Counts intelligently 2015-08-22 08:33:09 -04:00
Bertrand Haas f61529d254 Logit transform to MQ + jitter MQ capped improves VQSR 2015-08-20 17:53:01 -04:00
Ron Levine 900fe3f675 Merge pull request #1132 from broadinstitute/rhl_rev_htsjdk 
Move htsjdk & picard to rev 1.138
 2015-08-20 11:58:41 -04:00
Bertrand Haas eae4c875a9 Logistic transform of MQ + jitter to capped MQ in VariantDataManager 2015-08-20 11:10:45 -04:00
Ron Levine beec624a63 Move htsjdk & picard to rev 1.138 2015-08-20 10:42:25 -04:00
Geraldine Van der Auwera 5a875cb841 Fixed missing code tag 2015-08-14 14:58:28 -04:00
Geraldine Van der Auwera 19bbe45cbc Updated licenses for 2015 2015-08-06 15:23:11 -04:00
David Benjamin 5fcc3788bd UnifiedGenotypingEngine queries VariantContext for model if not given 2015-08-05 15:30:37 -04:00
Eric Banks df033f674d Patch for the incorrect "fixing" of mates when supplementary alignments are present. 
Note that this patch involves ignoring supplementary alignments.  Ideally we would want
to fix their mates properly but that would require a major refactoring of this soon-to-be
deprecated tool.
 2015-08-05 12:55:39 -04:00
vruano 604fb7aaf8 Faster implementation of the active state profile value calculation when running HC with a single sample. 
Find out about a dev-bug and added TODOs (reported in #1096).

Addresses issue #1095.

Conflicts:
	protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
 2015-07-30 10:56:05 -04:00
Valentin Ruano Rubio bb4c9fa1d3 Merge pull request #1099 from broadinstitute/vrr_magic_numbers 
Extracted some constant expressions involved HC variation discovery a…
 2015-07-29 13:38:23 -04:00
vruano 02c7876c72 Extracted some constant expressions involved HC variation discovery and genotyping. 
Addreses issue #1092.
 2015-07-29 11:58:13 -04:00
meganshand 4d4de27ba3 Removes unique(int maxSize) from KBestHaplotypeFinder 2015-07-28 15:54:21 -04:00
Valentin Ruano Rubio 3a3ff558c4 Merge pull request #1085 from broadinstitute/vrr_path_builder 
ReferenceConfidenceModel likelihood calculation in non…
 2015-07-28 10:48:03 -04:00
Geraldine Van der Auwera 43a37fc746 Merge pull request #1075 from broadinstitute/ldg_bamoutDocs 
Add info about multiple input samples (as relevant for M2)
 2015-07-27 16:56:36 -04:00
vruano 8f6daf70db Refactoring of ReferenceConfidenceModel likelihood calculation in non variant sites 
Changed a division by -10.0 to a multiplication by -.1 in QualUtils (typically multiplication is faster than division).

Addresses performance issue #1081.
 2015-07-26 08:33:46 -04:00
vruano 047aea9707 Address performance issue #1077 2015-07-23 13:44:10 -04:00
Laura Gauthier 85b340caed Add info about multiple input samples (as relevant for M2) 
Also generalize references to the tool/caller since this code is now shared by HC and M2
 2015-07-23 09:46:10 -04:00
Valentin Ruano Rubio 66cf22b28f Merge pull request #1069 from broadinstitute/vrr_ad_genotype_gvcfs_bugfix 
Fix AD propagation when subsetting alleles in non-diploid GenotypeGVCF.
 2015-07-22 18:53:43 -04:00
vruano 315e193e51 Fix AD propagation when subsetting alleles in non-diploid GenotypeGVCF. 
Addresses issue #913.

Also remove some commented out code and toxic debugging code that uses System.out/err.println.
 2015-07-22 17:08:13 -04:00
Geraldine Van der Auwera ca082bfb76 Updated license text and fixed a couple of typos in doc block 2015-07-21 17:55:48 -04:00