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
9d9827f176
Merge pull request #1031 from broadinstitute/lb_update_for_java8
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Updated gatk so it compiles with java 8
2015-07-28 11:09:19 -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
5939b4c100
Merge pull request #1073 from broadinstitute/ldg_SV-MVtestNameFix
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Fix logging name on SelectVariantsIntegrationTest::testInvertMendelia…
2015-07-27 16:54:59 -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
4fefedfb0b
Fix logging name on SelectVariantsIntegrationTest::testInvertMendelianViolationSelection()
2015-07-23 09:48:15 -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
75081bee2b
Merge pull request #1068 from broadinstitute/gvda_remove_beagle_walkers_971
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Removed walkers for handling Beagle data
2015-07-22 15:47:19 -04:00
3bd988825f
Removed walkers for handling Beagle data
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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
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
a4dde8f500
Merge pull request #1040 from broadinstitute/rhl_fasta_ref_maker
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Merge contiguous intervals properly, closes #1035
2015-07-21 14:19:09 -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
6e46b3696e
Merge contiguous intervals properly
2015-07-14 15:23:37 -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
e1c41b2c38
Updated gatk so it compiles on java 8
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updated cofoja to 1.2 from 1.0
added explicit type casts in places that java 8 required them
2015-06-26 15:59:46 -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
697c4b0cf1
Added else clause to handle symbolic alleles
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Add test for createAlleleMapping
2015-06-17 10:52:56 -04:00
29ebfc32c3
Merge pull request #1020 from broadinstitute/eb_handle_multiple_spanning_dels
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Handle cases where a given sample has multiple spanning deletions.
2015-06-16 14:20:46 -04:00
fe0b5e0fbe
Handle cases where a given sample has multiple spanning deletions.
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When a sample has multiple spanning deletions and we are asked to assign
likelihoods to the spanning deletion allele, we currently choose the first
deletion. Valentin pointed out that this isn't desired behavior. I
promised Valentin that I would address this issue, so here it is.
I do not believe that the correct thing to do is to sum the likelihoods
over all spanning deletions (I came up with problematic cases where this
breaks down).
So instead I'm using a simple heuristic approach: using the hom alt PLs, find
the most likely spanning deletion for this position and use its likelihoods.
In the 10K-sample VCF from Monkol there were only 2 cases that this problem
popped up. In both cases the heuristic approach works well.
2015-06-16 12:20:43 -04:00
Eric Banks
ldgauthier
Ron Levine
Samuel Lee
Mark Fleharty
Bertrand Haas
Geraldine Van der Auwera
David Benjamin
vruano
Valentin Ruano Rubio
meganshand
Louis Bergelson
Joseph White