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Deprecate tools that were outdated or redundant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
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
b0dea2ccca
Merge pull request #1150 from broadinstitute/eb_keep_iupac_in_IR
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Don't have the Indel Realigner change IUPAC reference bases.
2015-09-04 13:43:34 -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
cad81a6181
Merge pull request #1149 from broadinstitute/ldg_fixCGPbugForAndrea
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Fix bug when using --ignoreInputSamples
2015-09-04 11:17:15 -04:00
29ac64f6ce
Calculate GenotypeAnnotations before InfoFieldAnnotations
2015-09-03 09:22:46 -04:00
4769ef8dad
Fix bug when using --ignoreInputSamples
2015-09-02 09:27:06 -04:00
41256e1405
Added file-extension--dependent interval-list output to RealignerTargetCreator.
2015-08-31 11:22:18 -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
f61529d254
Logit transform to MQ + jitter MQ capped improves VQSR
2015-08-20 17:53:01 -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
beec624a63
Move htsjdk & picard to rev 1.138
2015-08-20 10:42:25 -04:00
5a875cb841
Fixed missing code tag
2015-08-14 14:58:28 -04:00
19bbe45cbc
Updated licenses for 2015
2015-08-06 15:23:11 -04:00
5fcc3788bd
UnifiedGenotypingEngine queries VariantContext for model if not given
2015-08-05 15:30:37 -04:00
df033f674d
Patch for the incorrect "fixing" of mates when supplementary alignments are present.
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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
604fb7aaf8
Faster implementation of the active state profile value calculation when running HC with a single sample.
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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
bb4c9fa1d3
Merge pull request #1099 from broadinstitute/vrr_magic_numbers
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Extracted some constant expressions involved HC variation discovery a…
2015-07-29 13:38:23 -04:00
02c7876c72
Extracted some constant expressions involved HC variation discovery and genotyping.
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Addreses issue #1092 .
2015-07-29 11:58:13 -04:00
4d4de27ba3
Removes unique(int maxSize) from KBestHaplotypeFinder
2015-07-28 15:54:21 -04:00
3a3ff558c4
Merge pull request #1085 from broadinstitute/vrr_path_builder
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ReferenceConfidenceModel likelihood calculation in non…
2015-07-28 10:48:03 -04:00
43a37fc746
Merge pull request #1075 from broadinstitute/ldg_bamoutDocs
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Add info about multiple input samples (as relevant for M2)
2015-07-27 16:56:36 -04:00
8f6daf70db
Refactoring of ReferenceConfidenceModel likelihood calculation in non variant sites
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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
047aea9707
Address performance issue #1077
2015-07-23 13:44:10 -04:00
85b340caed
Add info about multiple input samples (as relevant for M2)
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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
66cf22b28f
Merge pull request #1069 from broadinstitute/vrr_ad_genotype_gvcfs_bugfix
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Fix AD propagation when subsetting alleles in non-diploid GenotypeGVCF.
2015-07-22 18:53:43 -04:00
315e193e51
Fix AD propagation when subsetting alleles in non-diploid GenotypeGVCF.
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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
ca082bfb76
Updated license text and fixed a couple of typos in doc block
2015-07-21 17:55:48 -04:00
9360e1d293
Merge pull request #1059 from broadinstitute/vrr_true_false_list_removal
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More efficient implementation of the indel read qualities recalculati…
2015-07-21 17:13:45 -04:00
82f1236633
More efficient implementation of the indel read qualities recalculation for the PCR error model.
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Addresses #1054 .
2015-07-21 14:25:11 -04:00
da0c8c73fb
Merge pull request #1055 from broadinstitute/ldg_TRAdocs
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Updated TandemRepeatAnnotator docs
2015-07-21 14:16:20 -04:00
8c18ead5e4
Clarify VCF version for supporting population alleles files
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Clarify DeNovoPrior definition on PbyT
2015-07-20 13:42:57 -04:00
7b29c55eb6
Updated TandemRepeatAnnotator docs
2015-07-17 17:26:56 -04:00
7f74303f2b
Removes a very inefficient way to iterate in ReferenceConfidenceModel.isReadInformativeAboutIndelsOfSize(...)
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Addresses performance issue #1048 .
2015-07-16 12:04:12 -04:00
c109a953f8
Merge pull request #1029 from broadinstitute/rhl_vqslod_definition
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Make VQSLOD definition accurate
2015-07-06 19:52:15 -04:00
1a7e83fa50
Merge if both GT are phased
2015-06-30 13:03:16 -04:00
f994220617
Update the allele remapping code to handle the new spanning deletion allele.
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Now that Ron updated the GATK so that we use star to represent spanning
deletions, we need to catch those cases in the code that remaps alleles.
Otherwise, we try to pad the stars and that's just bad.
Added test from actual failing data.
2015-06-29 17:58:22 -04:00
09686f4595
Make VQSLOD definition accurate
2015-06-25 16:47:50 -04:00
719bb15340
Merge pull request #1019 from broadinstitute/rhl_var_index_param_gz
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Indexing parameters not required if output file has the g.vcf.gz exte…
2015-06-17 14:30:20 -04:00
Geraldine Van der Auwera
Yossi Farjoun
David Roazen
Laura Gauthier
vruano
Eric Banks
Ron Levine
Samuel Lee
meganshand
Mark Fleharty
Bertrand Haas
David Benjamin
Valentin Ruano Rubio