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Branch: master
Commits on Jul 9, 2015
  1. @vdauwera
Commits on Jul 7, 2015
  1. @kcibul

    Merge pull request #1022 from broadinstitute/kc_m2_pon

    kcibul authored
    update results of NA12878 using official ICE PON (same git hash for t…
  2. @kcibul

    Merge pull request #1037 from broadinstitute/ldg_M2_contaminationAnal…

    kcibul authored
    …ysis
    
    Document contamination downsampling analysis
Commits on Jul 6, 2015
  1. @vdauwera

    Merge pull request #1029 from broadinstitute/rhl_vqslod_definition

    vdauwera authored
    Make VQSLOD definition accurate
  2. @ldgauthier

    Document contamination downsampling analysis

    ldgauthier authored
    Add Yossi's Queue script to create synthetic contamination data
Commits on Jul 4, 2015
  1. @kcibul

    Merge pull request #1028 from broadinstitute/kc_oxog_fixes

    kcibul authored
    Fix Foxog NaN output and add read stats for indels
Commits on Jul 3, 2015
  1. @kcibul

    fixes NaN output in Foxog (github issue 1025) and also emit read dire…

    kcibul authored
    …ctions stats for indels (issue 1024)
    
    fixed docs
Commits on Jul 1, 2015
  1. @eitanbanks

    Merge pull request #1030 from broadinstitute/rhl_incorrect_rbp

    eitanbanks authored
    Merge if both GT are phased
Commits on Jun 30, 2015
  1. @ronlevine

    Merge if both GT are phased

    ronlevine authored
  2. @eitanbanks

    Merge pull request #1033 from broadinstitute/eb_fix_spanning_dels_wit…

    eitanbanks authored
    …h_new_allele
    
    Update the allele remapping code to handle the new spanning deletion allele.
Commits on Jun 29, 2015
  1. @eitanbanks

    Update the allele remapping code to handle the new spanning deletion …

    eitanbanks authored
    …allele.
    
    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.
Commits on Jun 25, 2015
  1. @ronlevine
Commits on Jun 17, 2015
  1. @vdauwera

    Merge pull request #1019 from broadinstitute/rhl_var_index_param_gz

    vdauwera authored
    Indexing parameters not required if output file has the g.vcf.gz exte…
  2. @eitanbanks

    Merge pull request #1014 from broadinstitute/gg_fix_combinevariants_d…

    eitanbanks authored
    …el_allele_1000
    
    Added else clause to handle symbolic alleles
  3. @vdauwera @ronlevine

    Added else clause to handle symbolic alleles

    vdauwera authored ronlevine committed
    Add test for createAlleleMapping
Commits on Jun 16, 2015
  1. @eitanbanks

    Merge pull request #1020 from broadinstitute/eb_handle_multiple_spann…

    eitanbanks authored
    …ing_dels
    
    Handle cases where a given sample has multiple spanning deletions.
  2. @eitanbanks

    Handle cases where a given sample has multiple spanning deletions.

    eitanbanks authored
    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.
  3. @kcibul
Commits on Jun 15, 2015
  1. @kcibul

    Merge pull request #1017 from broadinstitute/ldg_contaminationDS

    kcibul authored
    Enable contamination correction via downsampling (as for HaplotypeCal…
  2. @ldgauthier

    Enable contamination correction via downsampling (as for HaplotypeCal…

    ldgauthier authored
    …ler), added test
    
    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
Commits on Jun 14, 2015
  1. @eitanbanks

    Merge pull request #1016 from broadinstitute/rhl_allele_rep_span_dels

    eitanbanks authored
    Add spannning deletions allele
Commits on Jun 13, 2015
  1. @ronlevine
Commits on Jun 12, 2015
  1. @ronlevine
  2. @vdauwera

    Merge pull request #1001 from broadinstitute/jw_clarify_overlaping_co…

    vdauwera authored
    …ntigs
    
    Changed error message for Contigs Out of Order
  3. @whitejo

    Changed error message for Contigs Out of Order

    whitejo authored
    Changed confusing error message for out of order contigs
    
    Updated Exception message.
Commits on Jun 10, 2015
  1. @vdauwera

    Merge pull request #1009 from broadinstitute/gg_patch_depthofcoverage…

    vdauwera authored
    …_#1002
    
    User (mnw21cam) patch to fix DoC slowdown in 3.4
Commits on Jun 9, 2015
  1. @kcibul

    Merge pull request #1005 from broadinstitute/kc_m2_pon

    kcibul authored
    created panel of normals queue creation script and instructions
Commits on Jun 8, 2015
  1. @droazen

    Merge pull request #1012 from broadinstitute/rhl_build_vec_pairhmm_lib

    droazen authored
    Built VectorLoglessPairHMM lib with icc with gcc 4.4.7
Commits on Jun 6, 2015
  1. @vdauwera @ronlevine

    User (mnw21cam) patch to fix DoC slowdown in 3.4

    vdauwera authored ronlevine committed
Commits on Jun 5, 2015
  1. @lbergelson

    Merge pull request #1013 from lbergelson/patch-1

    lbergelson authored
    fix typo in queue arguments
  2. @lbergelson
  3. @ronlevine
Commits on Jun 4, 2015
  1. @droazen

    Merge pull request #999 from broadinstitute/rhl_load_vector_pair_hmm

    droazen authored
    Fix loading of VectorLoglessPairHMM by rolling back to Intel's lib version
Commits on Jun 2, 2015
  1. @kcibul

    created panel of normals queue creation script and instructions

    kcibul authored
    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
Commits on May 23, 2015
  1. @vdauwera

    Merge pull request #985 from broadinstitute/sa_refactor_cleansing_hac…

    vdauwera authored
    …k_negative_zeros_973_depends_on_841
    
    removed in-line conditional (hack) that changed the result from 0.0 to -0.0; see issue #841
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