c040da427d
Replace string literals for annotation groups. Closes #1216 .
2016-04-19 15:54:44 -04:00
d573fc4adf
Add some comments to AFCalculationResult
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Add note that VC may be null (in this case because there are too many alts)
Add todo for possible inefficient code
2016-04-04 09:35:54 -04:00
017828e4b7
Use the older murmur hash implementation that is included in the gatk jar.
2016-03-29 10:20:44 -04:00
c81795cf50
Fix license in DroppedReadsTracker.
2016-03-22 13:39:13 -04:00
a8ebf21ac3
Implementation of dropped read tracking.
2016-03-21 18:36:29 -04:00
b873467756
Merge pull request #1321 from broadinstitute/rhl_fix_hr_logger_name
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Change logger class to HomopolymerRun
2016-03-16 11:44:40 -04:00
5c0e97def4
Change logger class to HomopolymerRun
2016-03-16 10:01:21 -04:00
9ffdfeccd5
Add test case for fix
2016-03-15 11:06:48 -04:00
31fc64f82c
To address weird case with all hom-refs, but alt allele is present, skip AS_QD for all-ref sites and remove raw annotations whether or not they can be successfully finalized
2016-03-15 09:34:47 -04:00
6d7ec7377c
Set --reference_window_stop if homopolymer is greater than window size
2016-03-14 18:09:41 -04:00
c81d5b898e
Clarify VQSR inputs documentation
2016-03-11 16:38:33 -05:00
4990ed706a
Fixup for licensing update
2016-03-11 16:23:02 -05:00
d0432713e0
Merge pull request #1311 from broadinstitute/ldg_BetaTestAnnotationsGroup
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Add classes from "annotation party" to BetaTesting group
2016-03-11 08:13:32 -05:00
16ef36088e
Merge pull request #1308 from broadinstitute/gvda_fix_license_quotes_#1307
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Update licenses
2016-03-10 12:37:53 -05:00
28cfb06513
Add AS_culprit and AS_VQSLOD to VCF header in ApplyRecalibration so output passes VCF validation
2016-03-09 08:22:58 -05:00
d9f9bd1d56
Add classes from "annotation party" to BetaTesting group
2016-03-09 08:17:44 -05:00
9a306ca221
Update licenses
2016-03-05 01:09:43 -08:00
2b70f14740
Misc documentation improvements
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Added caveat to VariantFiltration documentation
Fixed PON creation example in M2 doc
Improved MalformedReadFilter doc
Updated N CIGAR error message
2016-03-03 15:48:54 -08:00
625941dc50
Merge pull request #1290 from broadinstitute/rhl_sac_nonref
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StrandAlleleCountsBySample selects most likely only from VCF alleles
2016-02-29 17:05:57 -05:00
5e2ffc188b
Merge pull request #1295 from broadinstitute/rhl_sv_error_output_1194
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Correct error messages and error handling in multiple tools
2016-02-29 17:05:24 -05:00
40a5adf767
Change error output to use the correct argument
2016-02-29 13:21:03 -05:00
80a22aad77
StrandAlleleCountsBySample selects most likely only from VCF alleles
2016-02-29 12:41:55 -05:00
c7e0f5b225
Removes Dithering from Rank Sum Test
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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
243a0fcb74
Allele-specific insert size ranksum annotation
2016-01-28 16:03:57 -05:00
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
ab2f541d1f
Small optimizations to the joint calling code.
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Thanks to profiling I noticed that the determineCoefficient() method was being called too often.
Because it returns a constant result in half of the invocations, its value should be cached when possible.
Also, the various calls to getLog10Likelihoods() showed up in the profiler, so I pulled those out too.
All told, it speeds up the genotyping by about 10 percent according to the profiler.
2016-01-12 21:48:20 -05:00
1d72ab099c
Merge pull request #1247 from broadinstitute/ldg_VQSRmodelOutput
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Add optional argument for VQSR to output the model to a file as a GAT…
2016-01-05 08:35:18 -05:00
fa1d90d236
Merge consecutive SNPs on the same read
2016-01-04 13:48:59 -05:00
2ddc48914e
Add optional argument for VQSR to output the model to a file as a GATKReport
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GATKReport output also has mean and variance for annotation normalization info
2016-01-04 08:37:08 -05:00
71c6709765
Merge pull request #1145 from broadinstitute/ldg_M2_HapMapSensitivity
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Fix no-normal bug; add HapMap sensitivity benchmarking
2016-01-04 08:27:37 -05:00
aa5e88a393
Fix exception when writing gVCF to stdout
2015-12-29 15:30:53 -05:00
eb6bdb2a62
MQ of Mate RankSum annotation
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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
f9e9d2e273
Fix no-normal bug; add HapMap sensitivity benchmarking
2015-12-22 08:29:01 -05:00
bf875974d1
Prep MuTect2 and ContEst for release
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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
b0730c2b81
Merge pull request #1239 from broadinstitute/gvda_straggler_doc_fixes_1237
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Improve doc block of GatherBqsrReports
Annotation doc enhancements (QD, InbreedingCoeff, ExcessHet and AS versions where applicable)
2015-11-22 13:58:20 -05:00
a7748368f8
Yet more doc improvements prior to 3.5 release
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Improve doc block of GatherBqsrReports
Annotation doc enhancements (QD, InbreedingCoeff, ExcessHet and AS versions where applicable)
2015-11-22 10:59:24 -05:00
46ba0e519e
Restore FindCoveredIntervals + add docs
2015-11-22 10:19:04 -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
4da0d1300c
adding fraction informative reads annotation.
2015-11-18 08:39:47 -05:00
9d5be24778
Move GatherBqsrReports from private to protected
2015-11-10 17:40:58 -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
e3d5d96076
Added the AF indepdent calculator for any ploidy but seems that is not doing a good job for haploid
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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
2cc7de4886
Suppress emission of the scary warning message from genotyping to no more than once in
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anything but DEBUG logging mode. Otherwise it fills up our output logs.
2015-11-05 14:19:21 -05:00
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
792142ec50
Implement BaseCounts per-sample
2015-09-30 08:59:11 -04:00
0dacf60012
Changed calls for RGQ=0 from 0/0 to ./. in output of GenotypeGVCFs.
2015-09-23 15:35:09 -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
David Benjamin
Laura Gauthier
Chris Norman
Ron Levine
Geraldine Van der Auwera
meganshand
Takuto Sato
Eric Banks
Yossi Farjoun
David Roazen
vruano
Samuel Lee