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4618 Commits (bf875974d1b64acb5d5e6dcba416d17fc73e1ec0)

Author SHA1 Message Date
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 46ba0e519e Restore FindCoveredIntervals + add docs 2015-11-22 10:19:04 -05:00
Ron Levine 08a9c80559 Make the header sequence dictionary match reference 2015-11-21 19:12:37 -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Deprecate tools that were outdated or redundant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Geraldine Van der Auwera 1cf66addaa Deprecate tools that were outdated or redundant 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
Ron Levine 0b3b09e3ff Move htsjdk & picard to version 1.141 2015-11-20 16:26:26 -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
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
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meganshand b5165b8d30 Fix for out of date VCF version output 2015-11-03 17:35:47 -05:00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
ldgauthier 4fbcfc2e36 Merge pull request #1173 from broadinstitute/ldg_AS_annotations 
New map-combine-finalize annotation framework
 2015-10-27 12:04:56 -04:00
Mark Fleharty 19af5724c5 Fixed an NA12878 Knowledgebase test, and made the RDQ option for BQSR binning hidden 2015-10-27 09:44:26 -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
meganshand 0d936b28c4 Merge pull request #1178 from broadinstitute/ms_ROCCurve 
ROCCurve High Confidence Mode
 2015-10-22 09:19:13 -04:00
Ron Levine 795fe75886 Update doc for multiallelics, trimming is the default behavior 2015-10-22 04:04:09 -04:00
meganshand a57500b2fc ROCCurve High Confidence Mode 
Integration Tests

Updated test

Changed method

Minor changes

Changed whitespace

Fixed uncalled counts and 0 in R

Fixed ReadBackedPileUp

Removed imports and changed MD5

Fixed failing test

Adding vqslod color

Updating script to create KB

Fixing integration test now that the KB is bigger

Adressing comments
 2015-10-21 21:30:54 -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
Chris Norman e776502c49 Fix Sample mergeValues failure when merging identical string values (#1156). 2015-10-12 09:56:05 -04:00
Ron Levine 2bcded11cb VariantAnnotator checks alleles when annotationg with external resource 2015-10-08 17:01:30 -04:00
Ron Levine 033115eae0 Move htsjdk & picard to version 1.140 2015-10-08 10:42:05 -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
Khalid Shakir 384a09e991 Minor updates to previous ParallelShell commit. 
Changed `--maximumNumberOfJobsToRunConcurrently`/`-maxConcurrentRun` to `Option[Int]`.
Updated licenses.
Added basic tests.
Removed some IntelliJ warnings.
 2015-09-29 09:36:37 -03:00
Johan Dahlberg b045f2d4aa ParallelShell added as a new JobRunner 
The ParallelShell job runner will run jobs locally on one node concurrently as specified by the DAG, with the option to limit the maximum number of concurrently running jobs using the flag `maximumNumberOfJobsToRunConcurrently`.

Signed-off-by: Khalid Shakir <kshakir@broadinstitute.org>
 2015-09-29 09:36:37 -03:00
samuelklee 302a69d685 Merge pull request #1165 from broadinstitute/sl_fix_no_calls 
Changed calls for RGQ=0 from 0/0 to ./. in output of GenotypeGVCFs.
 2015-09-28 12:26:18 -04:00
Geraldine Van der Auwera 118c559278 Trivial doc typo fix 2015-09-25 18:15:29 -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
Ami Levy Moonshine 1ad00cc9d4 fix typo in the ASEReadCounter document 2015-09-21 15:30:06 -04:00
meganshand cdfe0d7b7c Adding PER_TARGET_COVERAGE option 
Comments addressed
 2015-09-18 09:34:51 -04:00
Ron Levine 3ecabf7e45 Allow overriding ValidateVariants' hard-coded cutoff for allele length 2015-09-17 10:49:14 -04:00
ldgauthier 5870225f83 Merge pull request #1153 from broadinstitute/ms_excess_het 
Excess Het P-value
 2015-09-15 11:52:25 -04:00
Khalid Shakir 24e24b9468 Using `SamIndexes.asBaiSeekableStreamOrNull()` to support `.cram.crai`. 
Updated other IntelliJ IDEA warnings in GATKBAMIndex.
Updated example .cram files to match versions generated by current GATK/HTSJDK.
Bumped HTSJDK and Picard to 1.139 releases.
Added support for using `-SNAPSHOT` of HTSJDK in the future.
 2015-09-14 12:20:36 -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 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
Ron Levine 29ac64f6ce Calculate GenotypeAnnotations before InfoFieldAnnotations 2015-09-03 09:22:46 -04:00
Laura Gauthier a86f3909ca Update md5s for BAM header version change in Queue test output 2015-08-28 14:19:25 -04:00
Laura Gauthier 3dc68732fb Little changes to M2 code and docs 
Make MQ threshold a parameter (compare to M1 by setting to zero)
Add logic for multiple alternate alleles in tumor
Exclude MQ0 normal reads from normal LOD calculation
Fix path errors in Dream_Evaluations.md
Move M2 eval scripts out of walkers package so they run
 2015-08-27 15:31:27 -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 158477ea6c Re-ran the updateAllLicenses.sh script 2015-08-21 11:32:51 -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