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
ce5ecf1383
Enable contamination correction via downsampling (as for HaplotypeCaller), added test
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Add oxoG read count annotation and add as default annotation
Add ##SAMPLE VCF header line in accordance with TCGA VCF spec, specifying "File" line in sample header with BAM file name and "SampleName" with BAM sample name (Don't print sample file path if --no_cmdline_in_header is specified to help with test consistency)
Turn on active region assembly-based physical phasing for M2
Clean up M2-related annotations so UG doesn't crash if M2 annotations are called
2015-06-15 07:59:15 -04:00
b35085ca28
Indexing parameters not required if output file has the g.vcf.gz extensionv
2015-06-13 11:46:56 -04:00
dbed660183
Add spannning deletions allele
2015-06-12 16:43:06 -04:00
526f7c0d07
Merge pull request #985 from broadinstitute/sa_refactor_cleansing_hack_negative_zeros_973_depends_on_841
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removed in-line conditional (hack) that changed the result from 0.0 to -0.0; see issue #841
2015-05-23 00:02:52 -04:00
dac0b8ddfc
Added QD calculation
2015-05-22 11:59:10 -04:00
a6ca97ef14
Site-level selection based on genotype filter status
2015-05-21 11:27:20 -04:00
8d25b2ba40
removed in-line conditional (hack) that changed the result from 0.0 to -0.0; see issue #841
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removed irrelevant -0 comments as specified in issue #841 but committed in #973
2015-05-16 23:12:09 -04:00
d1a7edd796
Update pom versions to mark the start of GATK 3.5 development
2015-05-15 00:44:54 -04:00
f19618653a
Update pom versions for the 3.4 release
2015-05-15 00:40:39 -04:00
caafe84e74
Rev htsjdk to version 1.132 and picard to version 1.131, and switch to using the versions in maven central
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-We now pull htsjdk and picard from maven central.
-Updated the GATK codebase as necessary to adapt to changes in the Feature
interface.
-Since VCFHeader now requires that all header lines have unique keys, uniquified
the keys of GVCFBlock header lines by including the min/max GQ in the key.
Updated MD5s accordingly.
-Other MD5s changed as a result of an htsjdk fix to eliminate "-0" in VCF output.
2015-05-14 15:26:23 -04:00
f6b3d8e862
Merge pull request #947 from broadinstitute/rhl_invert_selection
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Added --invert_selection flag for variant selection queries
2015-05-13 13:40:32 -04:00
c752b9bca6
Fixed a small feature/bug that I introduced with the spanning deletions genotyping.
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In the case where there's a low quality SNP under a spanning deletion in the gvcfs:
if the SNP is not genotyped by GenotypeGVCFs (because it's just noise) we were still
emitting a record with just the symbolic DEL allele (because that allele is high quality).
We no longer do that.
2015-05-13 11:19:40 -04:00
4a75d54e65
Added invert and exclude flags for variant selection queries
2015-05-12 15:08:28 -04:00
7a75f4ae79
Merge pull request #974 from broadinstitute/jw_Var2BinPEDSwap
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Correct errant array element swap in FAM file output.
2015-05-12 08:49:16 -04:00
53a34cea4a
Merge pull request #938 from broadinstitute/eb_fix_spanning_deletions_in_genotyping
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Added a fix for genotyping positions over spanning deletions.
2015-05-11 23:11:47 -04:00
abb6bc6f57
Correct errant array element swap in FAM file output.
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dad and mom are swapped; paternal first, then maternal
updated MD5 chksums for test files
remove commented lines
2015-05-11 20:45:50 -04:00
vruano
Valentin Ruano Rubio
meganshand
Louis Bergelson
Geraldine Van der Auwera
Laura Gauthier
Joseph White
Ron Levine
Eric Banks
Sheila Chandran
melonistic
David Roazen