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
d4423d8303
Merge pull request #1079 from broadinstitute/vrr_path_builder
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PathBuilder for linear time creation of Graph paths (quadratic currently).
2015-07-24 09:36:06 -04:00
047aea9707
Address performance issue #1077
2015-07-23 13:44:10 -04:00
c98be3dbd6
Merge pull request #1076 from broadinstitute/dr_move_swapext_to_utils
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Move swapExt() methods to QScriptUtils, have versions in QScript class call into the util versions
2015-07-23 12:07:45 -04:00
5fd3d2be76
Move swapExt() methods to QScriptUtils, have versions in QScript class call into the util versions
2015-07-23 10:23:55 -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
d89067c791
Merge pull request #1066 from broadinstitute/gvda_fix_TR_license_1065
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Updated license text and fixed a couple of typos in doc block
2015-07-22 12:28:05 -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
178bf12b27
Merge pull request #1046 from broadinstitute/rhl_catvariants_sort
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Fix for mis-sorted VCF files in CatVariants
2015-07-21 17:37:27 -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
4d9724df64
Merge pull request #1057 from broadinstitute/ldg_CGPvcfVerDoc
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Clarify VCF version for supporting population alleles files
2015-07-21 14:15:07 -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
b296576505
Merge pull request #1050 from broadinstitute/vrr_true_false_list_removal
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Removes a very inefficient way to iterate in ReferenceConfidenceModel…
2015-07-16 14:03:21 -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
8fc631b7ae
Fix for mis-sorted VCF files in CatVariants
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When using CatVariants, VCF files were being sorted solely on the base
pair position of the first record, ignoring the chromosome. This can
become problematic when merging files from different chromosomes,
espeically if you have multiple VCFs per chromosome.
As an example, assume the following 3 lines are all in separate files:
1 10
1 100
2 20
The merged VCF from CatVariants (without -assumeSorted) would read:
1 10
2 20
1 100
This has the potential to break tools that expect chromosomes to be
contiguous within a VCF file.
This commit changes the comparator from one of Pair<Integer, File> to
one of Pair<VariantContext, File>. We construct a
VariantContextComparator from the provided reference, which will sort
the first record by chromosome and position properly. Additionally, if
-assumeSorted is given, we simply use a null VariantContext as the first
record, which will all be equal (as all will be null)
2015-07-14 14:12:31 -04:00
45a1d82305
Merge pull request #1041 from broadinstitute/ldg_ContEst
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Ported latest (non-yet-public) ContEst into GATK-private
2015-07-10 19:42:03 -04:00
1159cb3aa9
Ported latest (non-yet-public) ContEst into GATK; verified results against Firehose version
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Change file paths to put ContEst stuff in cancer directory
2015-07-09 17:06:06 -04:00
8ea4dcab8d
Merge remote-tracking branch 'unstable/master'
2015-07-09 15:17:03 -04:00
00526d4624
Merge pull request #1022 from broadinstitute/kc_m2_pon
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update results of NA12878 using official ICE PON (same git hash for t…
2015-07-07 16:37:46 -04:00
e6dff9cc4e
Merge pull request #1037 from broadinstitute/ldg_M2_contaminationAnalysis
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Document contamination downsampling analysis
2015-07-07 16:36:52 -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
b6da9366a6
Document contamination downsampling analysis
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Add Yossi's Queue script to create synthetic contamination data
2015-07-06 12:42:13 -04:00
aaf4e33e15
Merge pull request #1028 from broadinstitute/kc_oxog_fixes
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Fix Foxog NaN output and add read stats for indels
2015-07-04 10:24:21 -04:00
fa04024303
fixes NaN output in Foxog (github issue 1025) and also emit read directions stats for indels (issue 1024)
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fixed docs
2015-07-03 08:44:17 -04:00
d8e5d663fd
Merge pull request #1030 from broadinstitute/rhl_incorrect_rbp
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Merge if both GT are phased
2015-06-30 21:13:45 -04:00
1a7e83fa50
Merge if both GT are phased
2015-06-30 13:03:16 -04:00
5ea2aff379
Merge pull request #1033 from broadinstitute/eb_fix_spanning_dels_with_new_allele
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Update the allele remapping code to handle the new spanning deletion allele.
2015-06-29 22:57:14 -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
a4987310ae
Merge pull request #1014 from broadinstitute/gg_fix_combinevariants_del_allele_1000
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Added else clause to handle symbolic alleles
2015-06-17 12:52:18 -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
7018fd7203
update results of NA12878 using official ICE PON (same git hash for the caller)
2015-06-16 10:09:36 -04:00
578d429348
Merge pull request #1017 from broadinstitute/ldg_contaminationDS
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Enable contamination correction via downsampling (as for HaplotypeCal…
2015-06-15 14:37:10 -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
Valentin Ruano Rubio
Geraldine Van der Auwera
vruano
Lee Lichtenstein
David Roazen
Laura Gauthier
Joseph White
Eric Banks
Ron Levine
John Wallace
kcibul