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  • aad89cd653 Merge pull request #1005 from broadinstitute/kc_m2_pon kcibul 2015-06-09 11:10:17 -0400
  • 5e3f3d69db Merge pull request #1012 from broadinstitute/rhl_build_vec_pairhmm_lib droazen 2015-06-08 15:25:57 -0400
  • 95f2899f05 User (mnw21cam) patch to fix DoC slowdown in 3.4 Geraldine Van der Auwera 2015-06-02 00:34:34 -0400
  • 588d6f1180 Merge pull request #1013 from lbergelson/patch-1 Louis Bergelson 2015-06-05 19:27:51 -0400
  • ebdda72c88 fix typo in queue arguments Louis Bergelson 2015-06-05 17:06:23 -0400
  • 40d8fb99a3 Built VectorLoglessPairHMM lib with icc with gcc 4.4.7 Ron Levine 2015-06-05 15:38:25 -0400
  • 847c832ef9 Merge pull request #999 from broadinstitute/rhl_load_vector_pair_hmm droazen 2015-06-04 12:54:59 -0400
  • 5ceb63cc35 created panel of normals queue creation script and instructions Kristian Cibulskis 2015-05-29 18:13:12 -0400
  • 526f7c0d07 Merge pull request #985 from broadinstitute/sa_refactor_cleansing_hack_negative_zeros_973_depends_on_841 Geraldine Van der Auwera 2015-05-23 00:02:52 -0400
  • 27d3bafcbd Merge pull request #997 from broadinstitute/eb_add_foreign_read_filter Eric Banks 2015-05-22 14:34:28 -0400
  • 8c81e7df95 Added a new filter that can be used to remove reads that are too small and overly clipped. Eric Banks 2015-05-21 12:54:42 -0400
  • 3b0cb028e6 Fix loading of VectorLoglessPairHMM by rolling back to Intel's lib version Ron Levine 2015-05-22 13:04:24 -0400
  • 7f306bc4b6 Merge pull request #980 from broadinstitute/Sheila_QD_Update Geraldine Van der Auwera 2015-05-22 12:04:43 -0400
  • dac0b8ddfc Added QD calculation Sheila Chandran 2015-05-12 18:11:20 -0400
  • e96e52ee9d Merge pull request #986 from broadinstitute/rhl_select_genotype_filter_status Geraldine Van der Auwera 2015-05-22 09:59:00 -0400
  • a6ca97ef14 Site-level selection based on genotype filter status Ron Levine 2015-05-15 10:15:42 -0400
  • 8d25b2ba40 removed in-line conditional (hack) that changed the result from 0.0 to -0.0; see issue #841 melonistic 2015-04-26 16:58:09 -0400
  • 28a7ea43ec Merge pull request #982 from broadinstitute/kc_fp_analysis kcibul 2015-05-15 07:45:20 -0400
  • 3b1ee17727 added "artifact detection mode" for PON creation added "str_contraction" artifact filter (improves specificity, especially in exomes) refactored out VCF constants and added descriptions Kristian Cibulskis 2015-04-15 22:23:54 -0400
  • d1a7edd796 Update pom versions to mark the start of GATK 3.5 development Geraldine Van der Auwera 2015-05-15 00:44:54 -0400
  • f19618653a Update pom versions for the 3.4 release Geraldine Van der Auwera 2015-05-15 00:40:39 -0400
  • 6c195ffcb1 Merge remote-tracking branch 'unstable/master' Geraldine Van der Auwera 2015-05-15 00:38:39 -0400
  • 8b20523f5e Merge pull request #979 from broadinstitute/ami-fixASE-bug Geraldine Van der Auwera 2015-05-14 21:09:52 -0400
  • dee66b06fa Merge pull request #978 from broadinstitute/dr_rev_htsjdk_and_picard Geraldine Van der Auwera 2015-05-14 21:08:19 -0400
  • caafe84e74 Rev htsjdk to version 1.132 and picard to version 1.131, and switch to using the versions in maven central David Roazen 2015-05-12 15:05:40 -0400
  • f6b3d8e862 Merge pull request #947 from broadinstitute/rhl_invert_selection Geraldine Van der Auwera 2015-05-13 13:40:32 -0400
  • 5652cc6b5a Merge pull request #981 from broadinstitute/eb_no_lone_dels Eric Banks 2015-05-13 13:27:16 -0400
  • c752b9bca6 Fixed a small feature/bug that I introduced with the spanning deletions genotyping. Eric Banks 2015-05-13 11:10:23 -0400
  • 536d550794 solve bug - now work also when the reads does not have mate reads with no mate will be counted as valid reads Ami Levy-Moonshine 2015-03-31 15:08:25 -0400
  • 4a75d54e65 Added invert and exclude flags for variant selection queries Ron Levine 2015-03-29 11:55:15 -0400
  • 7a75f4ae79 Merge pull request #974 from broadinstitute/jw_Var2BinPEDSwap Geraldine Van der Auwera 2015-05-12 08:49:16 -0400
  • 53a34cea4a Merge pull request #938 from broadinstitute/eb_fix_spanning_deletions_in_genotyping Eric Banks 2015-05-11 23:11:47 -0400
  • abb6bc6f57 Correct errant array element swap in FAM file output. Joseph White 2015-04-26 16:17:41 -0400
  • 530e0e5ea6 Added a fix for combining/genotyping positions over spanning deletions. Eric Banks 2015-04-15 15:12:41 -0400
  • f77cee5171 Merge pull request #948 from broadinstitute/jw_deprecate_merge_var Geraldine Van der Auwera 2015-05-11 09:30:23 -0400
  • 5be8bc5dfc Deprecate --mergeVariantsViaLD in HC Joseph White 2015-04-26 17:32:08 -0400
  • 8a4a4f3fcf Merge pull request #968 from broadinstitute/gg_unexclude_annotations_#966 Geraldine Van der Auwera 2015-05-03 21:25:55 +0200
  • 5d8b9a7c20 Moved MQ0 out of HC exclusion and into StandardUGAnnotation Geraldine Van der Auwera 2015-05-03 01:04:49 +0200
  • 071d82d1bf Un-exclude SD and TRA from HC annotators; resolves #966 Exclude MQ0BySample Move SD and TRA to new StandardUGAnnotation interface There is now annotation interface (StandardUGAnnotation) holding annots that are standard in UG but should't be used as they are now with HC. This allows us to not have to exclude these annotations explicitly in HC, but still be able to use them for development purposes. Geraldine Van der Auwera 2015-05-01 22:15:00 +0200
  • e49f6dfd0f Merge pull request #970 from broadinstitute/gg_minor_docfixes Geraldine Van der Auwera 2015-05-03 00:36:12 +0200
  • 919c3eaa2e Numerous doc fixes; mostly formatting and clarifications Geraldine Van der Auwera 2015-04-30 03:58:44 +0200
  • fddc5331e1 Merge pull request #965 from broadinstitute/gg_nsubtil_clamp_hmm_fix Geraldine Van der Auwera 2015-05-01 22:18:20 +0200
  • 4b55118822 Merge pull request #967 from broadinstitute/rhl_va_allele_trim ldgauthier 2015-04-30 09:48:32 -0400
  • 9ff827c83a More allele trimming for VariantAnnotator Ron Levine 2015-04-29 20:28:28 -0400
  • f2b34d0823 Clamp the HMM window starting coordinate to 1 instead of 0 Geraldine Van der Auwera 2015-04-30 01:37:20 +0200
  • 9c2dd29bd0 Merge pull request #952 from broadinstitute/dr_queue_qsub_broad droazen 2015-04-27 20:24:50 -0400
  • 19ceca5e86 Queue: add -qsub-broad argument David Roazen 2015-04-23 13:46:16 -0400
  • cb4c3ea09e Merge pull request #943 from broadinstitute/ldg_fixAllowNonUniqueKmers Geraldine Van der Auwera 2015-04-27 04:08:50 +0200
  • 97caf94807 Fix implementation of allowNonUniqueKmersInRef so that it applies to all kmer sizes Laura Gauthier 2015-04-23 13:01:47 -0400
  • d4753f189f Merge pull request #930 from broadinstitute/rhl_bad_edge_pileup Eric Banks 2015-04-21 19:02:14 -0400
  • d5f98e99f0 Bypass reads with a bad CIGAR length Ron Levine 2015-04-10 09:48:35 -0400
  • bfcac455c9 Merge pull request #932 from broadinstitute/yf_fix_picard_md Geraldine Van der Auwera 2015-04-16 12:08:39 -0400
  • 8329fe46d1 Merge pull request #934 from broadinstitute/ks_cat_variants_extensions kshakir 2015-04-15 11:44:56 -0300
  • 90b579c78e CatVariants now allows different input / output file types. Escaping the CatVariantsIntegrationTest classpaths for possible spaces in the directory names. Khalid Shakir 2015-04-13 14:39:46 -0300
  • a7487e282a since Picard mark duplicates moved to a different package, this class was broken. here's the fix. it would be good to have tests for all the scala picard-wrappers, but that is out of scope for this commit. Yossi Farjoun 2015-04-13 08:44:30 -0400
  • 6adf91d49f Merge pull request #922 from broadinstitute/kc_refactor_acs kcibul 2015-04-08 09:52:11 -0400
  • 45610a142c initial refactoring of arguments into individual argument collections Kristian Cibulskis 2015-04-06 16:44:51 -0400
  • 2053afe52a Merge pull request #914 from broadinstitute/ldg_fixDitheringRandomness Geraldine Van der Auwera 2015-04-06 15:40:30 -0400
  • 7cc802f3d0 Merge pull request #915 from broadinstitute/yf_fix_missing_filename_in_error Geraldine Van der Auwera 2015-04-06 15:33:22 -0400
  • d30a6258bc added the missing file to the error message Yossi Farjoun 2015-04-03 11:13:02 -0400
  • 9c842df3a3 Initialize annotations so that --disableDithering actually works Laura Gauthier 2015-04-01 20:17:03 -0400
  • 761e456d07 Merge pull request #911 from broadinstitute/ab_vcf_cmd_line_header_909 droazen 2015-04-02 16:52:42 -0400
  • 024ec69e97 Modify GATK command line header for unique keys Alex Baumann 2015-03-31 13:47:29 -0400
  • c2c0037969 Merge pull request #910 from broadinstitute/rhl_mv_example_doc Geraldine Van der Auwera 2015-04-01 14:12:47 -0400
  • fe87484074 Update -mv example documentation Ron Levine 2015-03-30 21:41:17 -0400
  • d7f7022dce Merge pull request #904 from broadinstitute/pd_orig_dp Geraldine Van der Auwera 2015-03-30 09:01:33 -0400
  • 0101003138 Merge pull request #899 from broadinstitute/ldg_M2_tandemRepeatsAndContamination ldgauthier 2015-03-30 07:58:35 -0400
  • 87b3dddb39 Merge pull request #894 from broadinstitute/gg_ami_docs_license Geraldine Van der Auwera 2015-03-28 13:15:24 -0400
  • 9a73196813 Fix license Laura Gauthier 2015-03-25 09:43:37 -0400
  • 5a10758e2e Annotation changes for M2: Build a ReferenceContext in ActiveRegionWalkers to pass in to annotation engine so we can call the TandemRepeatAnnotator from M2 Make TandemRepeatAnnotator default annotation for M2. Setup (but don't use yet) HC-style contamination downsampling. New HC integration test with TandemRepeatAnnotator Laura Gauthier 2015-02-20 10:00:22 -0500
  • 1f81c033f5 Merge pull request #890 from broadinstitute/rhl_writers_use_index_args droazen 2015-03-27 15:00:58 -0400
  • aef0a83c52 Automatically choose indexing strategy by file extension Ron Levine 2015-03-18 09:33:24 -0400
  • 9b812308b1 Edited ASEReadCounter documentation Geraldine Van der Auwera 2015-03-23 18:06:06 -0400
  • b47bebb5a3 Merge pull request #900 from broadinstitute/ami-fix-MQ-after-Indel-Realingment-palantir Geraldine Van der Auwera 2015-03-26 01:08:05 -0400
  • bb76821942 New (private) read filter that can revert the MQ of reads affected by indel realignment. In the process of realignment we add +10 to the MQ of each realigned read, breaking the MQ 60 cap. That may contribute to problems observed by Bertrand (a step in the ROC curve plot of the VQSR results) Ami Levy-Moonshine 2015-01-30 13:31:15 -0500
  • c97c253ec8 Added keepOriginalDP argument to SelectVariants Phillip Dexheimer 2015-03-25 22:45:31 -0400
  • a77c8dd421 Merge pull request #895 from broadinstitute/pd_indel_qd Geraldine Van der Auwera 2015-03-25 11:25:53 -0400
  • dfa18a8fc6 Merge pull request #887 from broadinstitute/pd_vcf_cmdline_hdr Geraldine Van der Auwera 2015-03-25 00:48:55 -0400
  • 9e63696315 Remove indel-length normalization of QD for GGVCFs * Fixes #848 * length normalization is now only applied if the annotation is calculated in UG Phillip Dexheimer 2015-03-18 22:37:33 -0400
  • 0a45b2d79d Merge pull request #883 from broadinstitute/rhl_hc_mq0 Geraldine Van der Auwera 2015-03-23 12:59:08 -0400
  • 244dbe8634 Merge pull request #886 from broadinstitute/ami-RNA-ASEtools-march2015 amilev 2015-03-21 18:31:24 -0400
  • c5fc5c4f8c create 2 new tools: - ASEReadCounter (public tool) replce Tuuli's script to produce the input to Manny's tool. It count the number of reads that support the ref allele and the alt allele, filtereing low qual reads and bases and keep only properPaired reads - ASECaller (private tool) take both RNA and DNA, and produce ontingencyTables ** still under development ** Ami Levy-Moonshine 2014-08-12 15:21:58 -0400
  • 3b567d7a98 Fixed logging of 'out' command line parameter in VCF headers Phillip Dexheimer 2015-03-18 23:12:13 -0400
  • 46668d469a Exclude MappingQualityZero from default annotations Ron Levine 2015-03-16 18:37:15 -0400
  • bf0c72aab0 Merge pull request #881 from broadinstitute/gg_fix_gsalib_failures Geraldine Van der Auwera 2015-03-17 07:47:18 -0400
  • a75e1d4ce4 Fixes the test that was failing due to gsalib build failure Geraldine Van der Auwera 2015-03-17 04:26:03 -0400
  • c374d126d7 Merge pull request #808 from broadinstitute/pd_gsalib_concordance Geraldine Van der Auwera 2015-03-17 00:05:30 -0400
  • 4d4d33404e Added gsa.reshape.concordance.table function to gsalib Phillip Dexheimer 2015-02-04 23:02:54 -0500
  • 517320092c Merge pull request #863 from broadinstitute/kc_m2_initial_commit Geraldine Van der Auwera 2015-03-13 21:05:39 -0400
  • ab1053e83c It compiles, and produces results! Kristian Cibulskis 2014-12-22 16:46:17 -0500
  • 1d39ed9156 Merge pull request #814 from broadinstitute/biocyberman_maven_patches Geraldine Van der Auwera 2015-03-13 16:26:02 -0400
  • 39a972f348 Merge pull request #872 from broadinstitute/eb_create_rgq_format_field Geraldine Van der Auwera 2015-03-13 13:59:53 -0400
  • 7681e89454 Merge pull request #869 from broadinstitute/gg_fix_vqsr_plots_GSA-860 Geraldine Van der Auwera 2015-03-13 10:46:55 -0400
  • 3276a964f4 Merge pull request #871 from broadinstitute/pd_queue_unmapped_regression Geraldine Van der Auwera 2015-03-13 10:42:52 -0400
  • 1ff9463285 Added the RGQ format annotation to monomorphic sites in the VCF output of GenotypeGVCFs. Eric Banks 2015-03-13 00:26:21 -0400
  • 6ffa295963 Regression: The new 'includeUnmapped' PartitionBy annotation was incorrectly set for HC Phillip Dexheimer 2015-03-12 23:34:02 -0400
  • aa4084d42f Switched VQSR tranches plot ordering rule Geraldine Van der Auwera 2015-03-12 19:57:03 -0400
  • f5ec870964 Merge pull request #867 from broadinstitute/eb_combinegvcfs_option_to_break_blocks ldgauthier 2015-03-12 16:16:03 -0400
  • ea8a1edeb6 Adding option to CombineGVCFs to have it break blocks at every N sites. Eric Banks 2015-03-12 13:29:52 -0400
  • 5673ba9209 Merge pull request #866 from broadinstitute/gg_public_doc_dir_GSA-838 Geraldine Van der Auwera 2015-03-12 13:28:31 -0400