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100 Commits (e34ec0fbbba2dc1d424449ed30dc3b53e4ce6f6f)

Author SHA1 Message Date
David Benjamin aecaa6d38e Allow GenotypeGVCFs to emit ref sites. 2016-04-27 15:53:44 -04:00
Ron Levine f337b45724 Move htsjdk and picard to version 2.0.0 
Conflicts:
	protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java
	protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java
	protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
	protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
 2016-04-25 14:51:25 -04:00
meganshand 509400495b Changes edge case calculation for RankSumTest #1341 2016-04-22 14:41:05 -04:00
Ron Levine e2828104b1 SelectVariants and VariantFiltration not updating AC, AN and AF for --setFilteredGtToNocall 2016-04-17 10:24:05 -04:00
Ron Levine 0eba8822e2 Change HashMap to LinkedHashMap for predictable iteration 2016-04-10 20:10:38 -04:00
Ron Levine e4003bc792 Add informative exceptions to getSAMFileSamples() 2016-03-31 13:41:11 -04:00
Ron Levine edc1b20132 Output a summary of WARN messages 2016-03-29 11:39:18 -04:00
Geraldine Van der Auwera 9a306ca221 Update licenses 2016-03-05 01:09:43 -08:00
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
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
Yossi Farjoun 7896055be3 - Fixed bug in GenomeLoc parser 
- Added a warning when two contigs are too similar that it might cause problems with parsing
- Added tests of modified parser and of warning.
 2016-02-02 06:53:22 -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
Geraldine Van der Auwera c93a611ea3 Remove unneeded dependency 
Addresses https://github.com/broadgsa/gatk/pull/15 for Guillermo
 2016-01-21 16:51:01 -05:00
Ron Levine ed933013fe Remove variant contig order check 2016-01-16 19:32:28 -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
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 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 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
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
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
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
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
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
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
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
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 beec624a63 Move htsjdk & picard to rev 1.138 2015-08-20 10:42:25 -04:00
Khalid Shakir 9bee183f6c Switched to using CRAM's SamReader.Indexing implementation. 
CRAM now requires .bai index, just like BAM.
Test updates:
- Updated existing MD5s, as TLEN has changed.
- Tests multiple contigs.
- Tests several intervals per contig.
- Tests when `.cram.bai` is missing, even when `.cram.crai` is present.
Updated gatk docs for CRAM support, including:
- Arguments that work for both BAM and CRAM listed as such.
- Arguments that don't work for CRAM either explicitly say "BAM" or "doesn't work for CRAM".
- Instructions on how to recreate a `.cram.bai` using cramtools.
Cleaned up IntelliJ IDEA warnings regarding `Arrays.asList()` -> `Collections.singletonList()`.
 2015-08-11 17:52:49 -03:00
Geraldine Van der Auwera 19bbe45cbc Updated licenses for 2015 2015-08-06 15:23:11 -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
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
Joseph White 3bd988825f Removed walkers for handling Beagle data 
Added deprecation statements to DeprecatedToolChecks.java
    Removed integration test for Beagle walker
    Added URL for Beagle documentation
 2015-07-21 18:36:08 -04:00
vruano 82f1236633 More efficient implementation of the indel read qualities recalculation for the PCR error model. 
Addresses #1054.
 2015-07-21 14:25:11 -04:00
Ron Levine 09686f4595 Make VQSLOD definition accurate 2015-06-25 16:47:50 -04:00