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  • 687d2d0244 Merge pull request #1144 from broadinstitute/ldg_fixQueueTestsAgain ldgauthier 2015-08-28 16:32:45 -0400
  • a86f3909ca Update md5s for BAM header version change in Queue test output Laura Gauthier 2015-08-28 11:05:10 -0400
  • 13c5a74cc7 Merge pull request #1051 from broadinstitute/ldg_M2_additionalFeatures kcibul 2015-08-28 10:25:23 -0400
  • 3dc68732fb Little changes to M2 code and docs Make MQ threshold a parameter (compare to M1 by setting to zero) Add logic for multiple alternate alleles in tumor Exclude MQ0 normal reads from normal LOD calculation Fix path errors in Dream_Evaluations.md Move M2 eval scripts out of walkers package so they run Laura Gauthier 2015-04-24 11:03:00 -0400
  • 2ac5051767 Merge pull request #1063 from broadinstitute/mf_BinnedBQSR Mark Fleharty 2015-08-25 10:17:58 -0400
  • be22884138 Merge pull request #1125 from broadinstitute/bh_ROCCurveNA12878_plots Bertrand 2015-08-24 15:33:56 -0400
  • 5a1dda8b5c Added plots to ROCCurveNA12878 output Bertrand Haas 2015-08-05 13:29:00 -0400
  • daeb55429e Adding Static Binning to BQSR Mark Fleharty 2015-07-10 23:46:36 -0400
  • 4c35c2676b Merge pull request #1036 from broadinstitute/rhl_subset_sac Ron Levine 2015-08-22 10:07:49 -0400
  • 2afe3f7a21 Make GenotypeGVCFs subset Strand Allele Counts intelligently Ron Levine 2015-06-18 12:45:14 -0400
  • 3b4760fb64 Merge pull request #1141 from broadinstitute/bh_fix_again_license Bertrand 2015-08-21 11:35:17 -0400
  • 158477ea6c Re-ran the updateAllLicenses.sh script Bertrand Haas 2015-08-21 11:32:51 -0400
  • 3f5a5c0a11 Merge pull request #1140 from broadinstitute/bh_ROC_NA12878 Bertrand 2015-08-20 18:01:46 -0400
  • f61529d254 Logit transform to MQ + jitter MQ capped improves VQSR Bertrand Haas 2015-08-20 14:16:05 -0400
  • 900fe3f675 Merge pull request #1132 from broadinstitute/rhl_rev_htsjdk Ron Levine 2015-08-20 11:58:41 -0400
  • c10fcae25d Merge pull request #1109 from broadinstitute/bh_ROC_NA12878 Bertrand 2015-08-20 11:18:10 -0400
  • eae4c875a9 Logistic transform of MQ + jitter to capped MQ in VariantDataManager Bertrand Haas 2015-02-12 12:34:16 -0500
  • beec624a63 Move htsjdk & picard to rev 1.138 Ron Levine 2015-08-12 17:48:57 -0400
  • cd9db60ce2 Merge pull request #1134 from broadinstitute/gvda_cgp_docfix_1131 Geraldine Van der Auwera 2015-08-14 14:59:13 -0400
  • 5a875cb841 Fixed missing code tag Geraldine Van der Auwera 2015-08-13 16:40:42 -0400
  • e89c510ac5 Merge pull request #1115 from broadinstitute/ms_wgsmetrics_wrapper meganshand 2015-08-14 10:25:31 -0400
  • 5c9935ba10 Adding CollectWgsMetrics wrapper for queue meganshand 2015-08-04 16:41:32 -0400
  • 69fd4af15a Merge pull request #1111 from jsilter/overclippedreadfilter_endsoption Yossi Farjoun 2015-08-12 10:43:52 -0400
  • 62625b4bc6 Add option to not require soft-clips on both ends Jacob Silterra 2015-08-12 10:38:27 -0400
  • d77611292f Merge pull request #1113 from broadinstitute/ks_cram_with_index kshakir 2015-08-11 21:47:10 -0300
  • 9bee183f6c Switched to using CRAM's SamReader.Indexing implementation. CRAM now requires .bai index, just like BAM. Test updates: - Updated existing MD5s, as TLEN has changed. - Tests multiple contigs. - Tests several intervals per contig. - Tests when `.cram.bai` is missing, even when `.cram.crai` is present. Updated gatk docs for CRAM support, including: - Arguments that work for both BAM and CRAM listed as such. - Arguments that don't work for CRAM either explicitly say "BAM" or "doesn't work for CRAM". - Instructions on how to recreate a `.cram.bai` using cramtools. Cleaned up IntelliJ IDEA warnings regarding `Arrays.asList()` -> `Collections.singletonList()`. Khalid Shakir 2015-08-02 10:50:39 -0300
  • 822d6e9b5b Merge pull request #1123 from broadinstitute/gvda_updatelicenses_1118 Geraldine Van der Auwera 2015-08-10 18:46:47 -0400
  • 19bbe45cbc Updated licenses for 2015 Geraldine Van der Auwera 2015-08-06 14:30:38 -0400
  • 9554e06952 Merge pull request #1119 from broadinstitute/db_diff_objects Geraldine Van der Auwera 2015-08-06 14:43:39 -0400
  • ddb01058d3 moved DiffObjects David Benjamin 2015-08-05 16:31:06 -0400
  • 893c09b6e0 Merge pull request #1107 from broadinstitute/db_issue_1052 David Benjamin 2015-08-05 21:16:29 -0400
  • 5fcc3788bd UnifiedGenotypingEngine queries VariantContext for model if not given David Benjamin 2015-07-30 11:58:07 -0400
  • c34d8174fc Merge pull request #1114 from broadinstitute/eb_fix_IR_secondary_mates Eric Banks 2015-08-05 14:13:24 -0400
  • df033f674d Patch for the incorrect "fixing" of mates when supplementary alignments are present. Eric Banks 2015-08-03 22:34:46 -0400
  • f73871c865 Merge pull request #1098 from broadinstitute/vrr_rcm_is_active_calculateGenotypes Valentin Ruano Rubio 2015-07-30 10:57:33 -0400
  • 604fb7aaf8 Faster implementation of the active state profile value calculation when running HC with a single sample. vruano 2015-07-29 16:52:11 -0400
  • 9819624801 Merge pull request #1105 from broadinstitute/gvda_typo_fixes_1087_1042 Geraldine Van der Auwera 2015-07-29 23:37:00 -0400
  • 875c7ffa1a Fixed typos and made some argument docs improvements Geraldine Van der Auwera 2015-07-29 18:57:59 -0400
  • bb4c9fa1d3 Merge pull request #1099 from broadinstitute/vrr_magic_numbers Valentin Ruano Rubio 2015-07-29 13:38:23 -0400
  • 02c7876c72 Extracted some constant expressions involved HC variation discovery and genotyping. vruano 2015-07-28 15:32:10 -0400
  • ac86b22662 Merge pull request #1101 from broadinstitute/ms_remove_KBest_unique Geraldine Van der Auwera 2015-07-28 17:27:48 -0400
  • 4d4de27ba3 Removes unique(int maxSize) from KBestHaplotypeFinder meganshand 2015-07-28 15:54:21 -0400
  • 9d9827f176 Merge pull request #1031 from broadinstitute/lb_update_for_java8 Louis Bergelson 2015-07-28 11:09:19 -0400
  • 3a3ff558c4 Merge pull request #1085 from broadinstitute/vrr_path_builder Valentin Ruano Rubio 2015-07-28 10:48:03 -0400
  • 43a37fc746 Merge pull request #1075 from broadinstitute/ldg_bamoutDocs Geraldine Van der Auwera 2015-07-27 16:56:36 -0400
  • 5939b4c100 Merge pull request #1073 from broadinstitute/ldg_SV-MVtestNameFix Geraldine Van der Auwera 2015-07-27 16:54:59 -0400
  • 8f6daf70db Refactoring of ReferenceConfidenceModel likelihood calculation in non variant sites vruano 2015-07-24 13:03:14 -0400
  • d4423d8303 Merge pull request #1079 from broadinstitute/vrr_path_builder Valentin Ruano Rubio 2015-07-24 09:36:06 -0400
  • 047aea9707 Address performance issue #1077 vruano 2015-07-23 12:15:23 -0400
  • c98be3dbd6 Merge pull request #1076 from broadinstitute/dr_move_swapext_to_utils Lee Lichtenstein 2015-07-23 12:07:45 -0400
  • 5fd3d2be76 Move swapExt() methods to QScriptUtils, have versions in QScript class call into the util versions David Roazen 2015-07-23 10:12:46 -0400
  • 4fefedfb0b Fix logging name on SelectVariantsIntegrationTest::testInvertMendelianViolationSelection() Laura Gauthier 2015-07-22 08:58:11 -0400
  • 85b340caed Add info about multiple input samples (as relevant for M2) Also generalize references to the tool/caller since this code is now shared by HC and M2 Laura Gauthier 2015-07-23 09:44:13 -0400
  • 66cf22b28f Merge pull request #1069 from broadinstitute/vrr_ad_genotype_gvcfs_bugfix Valentin Ruano Rubio 2015-07-22 18:53:43 -0400
  • 315e193e51 Fix AD propagation when subsetting alleles in non-diploid GenotypeGVCF. vruano 2015-07-22 13:17:17 -0400
  • 75081bee2b Merge pull request #1068 from broadinstitute/gvda_remove_beagle_walkers_971 Geraldine Van der Auwera 2015-07-22 15:47:19 -0400
  • d89067c791 Merge pull request #1066 from broadinstitute/gvda_fix_TR_license_1065 Geraldine Van der Auwera 2015-07-22 12:28:05 -0400
  • 3bd988825f Removed walkers for handling Beagle data Joseph White 2015-05-27 22:35:06 -0400
  • ca082bfb76 Updated license text and fixed a couple of typos in doc block Geraldine Van der Auwera 2015-07-21 17:55:48 -0400
  • 178bf12b27 Merge pull request #1046 from broadinstitute/rhl_catvariants_sort Eric Banks 2015-07-21 17:37:27 -0400
  • 9360e1d293 Merge pull request #1059 from broadinstitute/vrr_true_false_list_removal Valentin Ruano Rubio 2015-07-21 17:13:45 -0400
  • 82f1236633 More efficient implementation of the indel read qualities recalculation for the PCR error model. vruano 2015-07-20 17:02:53 -0400
  • a4dde8f500 Merge pull request #1040 from broadinstitute/rhl_fasta_ref_maker Geraldine Van der Auwera 2015-07-21 14:19:09 -0400
  • da0c8c73fb Merge pull request #1055 from broadinstitute/ldg_TRAdocs Geraldine Van der Auwera 2015-07-21 14:16:20 -0400
  • 4d9724df64 Merge pull request #1057 from broadinstitute/ldg_CGPvcfVerDoc Geraldine Van der Auwera 2015-07-21 14:15:07 -0400
  • 8c18ead5e4 Clarify VCF version for supporting population alleles files Clarify DeNovoPrior definition on PbyT Laura Gauthier 2015-07-20 13:22:40 -0400
  • 7b29c55eb6 Updated TandemRepeatAnnotator docs Laura Gauthier 2015-07-17 17:26:56 -0400
  • b296576505 Merge pull request #1050 from broadinstitute/vrr_true_false_list_removal Valentin Ruano Rubio 2015-07-16 14:03:21 -0400
  • 7f74303f2b Removes a very inefficient way to iterate in ReferenceConfidenceModel.isReadInformativeAboutIndelsOfSize(...) vruano 2015-07-15 17:58:51 -0400
  • 6e46b3696e Merge contiguous intervals properly Ron Levine 2015-07-06 12:30:53 -0400
  • 8fc631b7ae Fix for mis-sorted VCF files in CatVariants John Wallace 2015-05-21 11:58:53 -0400
  • 45a1d82305 Merge pull request #1041 from broadinstitute/ldg_ContEst ldgauthier 2015-07-10 19:42:03 -0400
  • 1159cb3aa9 Ported latest (non-yet-public) ContEst into GATK; verified results against Firehose version Laura Gauthier 2015-06-06 10:16:39 -0400
  • 8ea4dcab8d Merge remote-tracking branch 'unstable/master' Geraldine Van der Auwera 2015-07-09 15:17:03 -0400
  • 00526d4624 Merge pull request #1022 from broadinstitute/kc_m2_pon kcibul 2015-07-07 16:37:46 -0400
  • e6dff9cc4e Merge pull request #1037 from broadinstitute/ldg_M2_contaminationAnalysis kcibul 2015-07-07 16:36:52 -0400
  • c109a953f8 Merge pull request #1029 from broadinstitute/rhl_vqslod_definition Geraldine Van der Auwera 2015-07-06 19:52:15 -0400
  • b6da9366a6 Document contamination downsampling analysis Add Yossi's Queue script to create synthetic contamination data Laura Gauthier 2015-06-23 22:57:02 +0200
  • aaf4e33e15 Merge pull request #1028 from broadinstitute/kc_oxog_fixes kcibul 2015-07-04 10:24:21 -0400
  • fa04024303 fixes NaN output in Foxog (github issue 1025) and also emit read directions stats for indels (issue 1024) Kristian Cibulskis 2015-06-22 16:25:02 -0400
  • d8e5d663fd Merge pull request #1030 from broadinstitute/rhl_incorrect_rbp Eric Banks 2015-06-30 21:13:45 -0400
  • 1a7e83fa50 Merge if both GT are phased Ron Levine 2015-06-26 13:12:55 -0400
  • 5ea2aff379 Merge pull request #1033 from broadinstitute/eb_fix_spanning_dels_with_new_allele Eric Banks 2015-06-29 22:57:14 -0400
  • f994220617 Update the allele remapping code to handle the new spanning deletion allele. Eric Banks 2015-06-29 17:54:08 -0400
  • e1c41b2c38 Updated gatk so it compiles on java 8 Louis Bergelson 2015-06-26 15:59:46 -0400
  • 09686f4595 Make VQSLOD definition accurate Ron Levine 2015-06-25 10:17:29 -0400
  • 719bb15340 Merge pull request #1019 from broadinstitute/rhl_var_index_param_gz Geraldine Van der Auwera 2015-06-17 14:30:20 -0400
  • a4987310ae Merge pull request #1014 from broadinstitute/gg_fix_combinevariants_del_allele_1000 Eric Banks 2015-06-17 12:52:18 -0400
  • 697c4b0cf1 Added else clause to handle symbolic alleles Geraldine Van der Auwera 2015-06-10 11:52:13 -0400
  • 29ebfc32c3 Merge pull request #1020 from broadinstitute/eb_handle_multiple_spanning_dels Eric Banks 2015-06-16 14:20:46 -0400
  • fe0b5e0fbe Handle cases where a given sample has multiple spanning deletions. Eric Banks 2015-06-14 00:06:38 -0400
  • 7018fd7203 update results of NA12878 using official ICE PON (same git hash for the caller) Kristian Cibulskis 2015-06-16 10:09:36 -0400
  • 578d429348 Merge pull request #1017 from broadinstitute/ldg_contaminationDS kcibul 2015-06-15 14:37:10 -0400
  • ce5ecf1383 Enable contamination correction via downsampling (as for HaplotypeCaller), 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 Laura Gauthier 2015-05-21 15:57:55 -0400
  • 9522be8762 Merge pull request #1016 from broadinstitute/rhl_allele_rep_span_dels Eric Banks 2015-06-13 22:12:23 -0400
  • b35085ca28 Indexing parameters not required if output file has the g.vcf.gz extensionv Ron Levine 2015-06-12 22:03:23 -0400
  • dbed660183 Add spannning deletions allele Ron Levine 2015-06-01 11:25:10 -0400
  • 456fefa860 Merge pull request #1001 from broadinstitute/jw_clarify_overlaping_contigs Geraldine Van der Auwera 2015-06-12 15:03:10 -0400
  • 398dc7a123 Changed error message for Contigs Out of Order Joseph White 2015-05-25 00:22:31 -0400
  • 2a7f95eddb Merge pull request #1009 from broadinstitute/gg_patch_depthofcoverage_#1002 Geraldine Van der Auwera 2015-06-10 11:16:08 -0400