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
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
9522be8762
Merge pull request #1016 from broadinstitute/rhl_allele_rep_span_dels
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Add spannning deletions allele
2015-06-13 22:12:23 -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
456fefa860
Merge pull request #1001 from broadinstitute/jw_clarify_overlaping_contigs
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Changed error message for Contigs Out of Order
2015-06-12 15:03:10 -04:00
398dc7a123
Changed error message for Contigs Out of Order
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Changed confusing error message for out of order contigs
Updated Exception message.
2015-06-11 21:46:06 -04:00
2a7f95eddb
Merge pull request #1009 from broadinstitute/gg_patch_depthofcoverage_#1002
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User (mnw21cam) patch to fix DoC slowdown in 3.4
2015-06-10 11:16:08 -04:00
aad89cd653
Merge pull request #1005 from broadinstitute/kc_m2_pon
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created panel of normals queue creation script and instructions
2015-06-09 11:10:17 -04:00
5e3f3d69db
Merge pull request #1012 from broadinstitute/rhl_build_vec_pairhmm_lib
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Built VectorLoglessPairHMM lib with icc with gcc 4.4.7
2015-06-08 15:25:57 -04:00
95f2899f05
User (mnw21cam) patch to fix DoC slowdown in 3.4
2015-06-05 21:12:46 -04:00
588d6f1180
Merge pull request #1013 from lbergelson/patch-1
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fix typo in queue arguments
2015-06-05 19:27:51 -04:00
ebdda72c88
fix typo in queue arguments
2015-06-05 17:06:23 -04:00
40d8fb99a3
Built VectorLoglessPairHMM lib with icc with gcc 4.4.7
2015-06-05 15:38:25 -04:00
847c832ef9
Merge pull request #999 from broadinstitute/rhl_load_vector_pair_hmm
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Fix loading of VectorLoglessPairHMM by rolling back to Intel's lib version
2015-06-04 12:54:59 -04:00
5ceb63cc35
created panel of normals queue creation script and instructions
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increased runtime java memory, changed default PON for NN to be new ICE PON
updated FP rates, when using new default PON. SNPs up by ~3%, INDELs down by 40%
updated git hash reference
updated git hash reference
2015-06-02 16:23:10 -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
27d3bafcbd
Merge pull request #997 from broadinstitute/eb_add_foreign_read_filter
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Added a new filter that can be used to remove reads that are too smal…
2015-05-22 14:34:28 -04:00
8c81e7df95
Added a new filter that can be used to remove reads that are too small and overly clipped.
2015-05-22 14:33:35 -04:00
3b0cb028e6
Fix loading of VectorLoglessPairHMM by rolling back to Intel's lib version
2015-05-22 14:16:00 -04:00
7f306bc4b6
Merge pull request #980 from broadinstitute/Sheila_QD_Update
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Sheila qd update
2015-05-22 12:04:43 -04:00
dac0b8ddfc
Added QD calculation
2015-05-22 11:59:10 -04:00
Geraldine Van der Auwera
Laura Gauthier
Valentin Ruano Rubio
vruano
Ron Levine
kcibul
Eric Banks
Joseph White
droazen
Louis Bergelson
Sheila Chandran