46ba0e519e
Restore FindCoveredIntervals + add docs
2015-11-22 10:19:04 -05:00
08a9c80559
Make the header sequence dictionary match reference
2015-11-21 19:12:37 -05:00
22fa1511be
Merge pull request #1235 from broadinstitute/gvda_deprecate_useless_tools_1192
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Deprecate tools that were outdated or redundant
2015-11-21 14:58:00 -05:00
1cf66addaa
Deprecate tools that were outdated or redundant
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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
2570cab24c
Assorted documentation fixes, enhancements and reorganization.
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See issues referenced by the pull request for details.
2015-11-20 22:44:46 -05:00
0b3b09e3ff
Move htsjdk & picard to version 1.141
2015-11-20 16:26:26 -05:00
ccaddefa19
Validate VCF with sequence dictionary
2015-11-20 09:23:24 -05:00
4da0d1300c
adding fraction informative reads annotation.
2015-11-18 08:39:47 -05:00
25b8ba45f4
More allele-specific annotations: AS_QD and AS_InbreedingCoeff
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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
e4627ed5c3
Addressing comments
2015-11-04 11:00:01 -05:00
b5165b8d30
Fix for out of date VCF version output
2015-11-03 17:35:47 -05:00
3d1dc303b3
Merge pull request #1197 from broadinstitute/ts_ve_nullPointer
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Prevent null pointer exception in PrintMissingComp module
2015-11-02 14:42:50 -05:00
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
f7eb5d3082
Enable family-level stratification (if a ped file is provided)
2015-10-28 09:55:04 -04:00
4fbcfc2e36
Merge pull request #1173 from broadinstitute/ldg_AS_annotations
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New map-combine-finalize annotation framework
2015-10-27 12:04:56 -04:00
19af5724c5
Fixed an NA12878 Knowledgebase test, and made the RDQ option for BQSR binning hidden
2015-10-27 09:44:26 -04:00
fcaf37279c
Finished draft of code for new map-combine-reduce annotation framework
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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
36ca9fe898
Allow LeftAlignAndTrimVariants to handle alleles longer than the default processing window
2015-10-25 20:33:56 -04:00
0d936b28c4
Merge pull request #1178 from broadinstitute/ms_ROCCurve
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ROCCurve High Confidence Mode
2015-10-22 09:19:13 -04:00
795fe75886
Update doc for multiallelics, trimming is the default behavior
2015-10-22 04:04:09 -04:00
a57500b2fc
ROCCurve High Confidence Mode
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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
df7a482335
VariantAnnotator now supports annotating FILTER field from an external resource.
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Updated the docs.
2015-10-14 14:26:21 -04:00
e776502c49
Fix Sample mergeValues failure when merging identical string values ( #1156 ).
2015-10-12 09:56:05 -04:00
2bcded11cb
VariantAnnotator checks alleles when annotationg with external resource
2015-10-08 17:01:30 -04:00
033115eae0
Move htsjdk & picard to version 1.140
2015-10-08 10:42:05 -04:00
622ec352bb
Fix for combining records in which one has a spanning deletion and needs a padded reference allele.
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This was erroring out and not working.
2015-10-02 16:28:16 -04:00
506958a0b7
Implemented a new VariantEval evaulation module, MetricsCollection. Fixed null pointer exception, updated tests.
2015-09-30 17:21:30 -04:00
792142ec50
Implement BaseCounts per-sample
2015-09-30 08:59:11 -04:00
384a09e991
Minor updates to previous ParallelShell commit.
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Changed `--maximumNumberOfJobsToRunConcurrently`/`-maxConcurrentRun` to `Option[Int]`.
Updated licenses.
Added basic tests.
Removed some IntelliJ warnings.
2015-09-29 09:36:37 -03:00
b045f2d4aa
ParallelShell added as a new JobRunner
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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
302a69d685
Merge pull request #1165 from broadinstitute/sl_fix_no_calls
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Changed calls for RGQ=0 from 0/0 to ./. in output of GenotypeGVCFs.
2015-09-28 12:26:18 -04:00
118c559278
Trivial doc typo fix
2015-09-25 18:15:29 -04:00
0dacf60012
Changed calls for RGQ=0 from 0/0 to ./. in output of GenotypeGVCFs.
2015-09-23 15:35:09 -04:00
1ad00cc9d4
fix typo in the ASEReadCounter document
2015-09-21 15:30:06 -04:00
cdfe0d7b7c
Adding PER_TARGET_COVERAGE option
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Comments addressed
2015-09-18 09:34:51 -04:00
3ecabf7e45
Allow overriding ValidateVariants' hard-coded cutoff for allele length
2015-09-17 10:49:14 -04:00
5870225f83
Merge pull request #1153 from broadinstitute/ms_excess_het
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Excess Het P-value
2015-09-15 11:52:25 -04:00
24e24b9468
Using `SamIndexes.asBaiSeekableStreamOrNull()` to support `.cram.crai`.
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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
d767e1722e
Excess Het P-value
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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
53b506a0b8
Make sure inputPriors get used if they are specified
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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
83a7012d69
Mask snps with --snpmask
2015-09-09 16:20:48 -04:00
5f76ae6a37
Don't have the Indel Realigner change IUPAC reference bases.
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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
29ac64f6ce
Calculate GenotypeAnnotations before InfoFieldAnnotations
2015-09-03 09:22:46 -04:00
a86f3909ca
Update md5s for BAM header version change in Queue test output
2015-08-28 14:19:25 -04:00
3dc68732fb
Little changes to M2 code and docs
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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
daeb55429e
Adding Static Binning to BQSR
2015-08-24 13:36:17 -04:00
2afe3f7a21
Make GenotypeGVCFs subset Strand Allele Counts intelligently
2015-08-22 08:33:09 -04:00
158477ea6c
Re-ran the updateAllLicenses.sh script
2015-08-21 11:32:51 -04:00
900fe3f675
Merge pull request #1132 from broadinstitute/rhl_rev_htsjdk
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Move htsjdk & picard to rev 1.138
2015-08-20 11:58:41 -04:00
eae4c875a9
Logistic transform of MQ + jitter to capped MQ in VariantDataManager
2015-08-20 11:10:45 -04:00
Geraldine Van der Auwera
Ron Levine
meganshand
Yossi Farjoun
Laura Gauthier
Takuto Sato
Mark Fleharty
Chris Norman
Eric Banks
Kate Noblett
Khalid Shakir
Johan Dahlberg
samuelklee
Samuel Lee
Ami Levy Moonshine
Bertrand Haas