zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Commit Graph

  • f8a081a262 Updated readme in public/doc to just point to the website Geraldine Van der Auwera 2015-03-12 11:52:48 -0400
  • e1862a04a8 Merge pull request #862 from broadinstitute/rhl_doc_args_incompatibility Geraldine Van der Auwera 2015-03-11 13:08:53 -0400
  • bee7f655b7 Log a warning if using incompatible arguments in DepthOfCoverage Ron Levine 2015-03-07 21:53:32 -0500
  • 6645669eca Merge pull request #818 from broadinstitute/mf_CheckNameInAssessNA12878 ldgauthier 2015-03-10 10:33:05 -0400
  • 957946c73c Change to AssessNA12878 to allow for analysis of files that specify name differing from NA12878. Mark Fleharty 2015-03-02 15:18:17 -0500
  • 4bff024107 Merge pull request #819 from broadinstitute/rhl_fix_docs_npa_filter Geraldine Van der Auwera 2015-03-06 07:46:33 -0500
  • 71d68c3d93 Fix NotPrimaryAlignmentFilter documentation Ron Levine 2015-03-05 20:30:46 -0500
  • ff6e288241 Upgrade SLF4J to allow new convient logging syntaxes biocyberman 2015-02-13 00:27:38 +0100
  • f8f2680142 Merge pull request #812 from broadinstitute/ldg_combineData_submit Valentin Ruano Rubio 2015-03-02 15:12:31 -0500
  • 83bd85d8de Merge pull request #817 from broadinstitute/ldg_fixQueueTests ldgauthier 2015-03-02 09:49:17 -0500
  • aaf952469e Change UG @PartitionBy to fix Queue tests Laura Gauthier 2015-03-01 14:31:08 -0500
  • 6ebcba5234 New walker to combine data for different formats of same sample that were called and VQSRed together; has functionality to combine only specified samples, omitting others (e.g. combine the uniquified NA12878s with -usn NA12878.variant51 -usn NA12878.variant102) GenotypeGVCFs now has the ability to unique-ify samples so I can genotype together two different datasets containing the same sample Modify InbreedingCoeff so that it works when genotyping uniquified samples Laura Gauthier 2014-09-24 08:41:12 -0400
  • 2d992ad818 Modify assessment/site reporting criteria for better bookkeeping Make sure -allSites outputs TPs that have discordance genotypes (although we won't know they're discordant) Make AssessNA12878 output report record the name of the VCF from which the assessment was derived Laura Gauthier 2014-09-24 11:23:51 -0400
  • 8efaa97d84 Merge pull request #815 from broadinstitute/ldg_updateMulitallelicVAtestData ldgauthier 2015-03-01 12:10:25 -0500
  • 21390575dd Merge pull request #816 from broadinstitute/rhl_gc_content_value_type Geraldine Van der Auwera 2015-02-26 15:26:28 -0500
  • 44e5965a4b Change GC Content value type from Integer to Float Ron Levine 2015-02-24 13:06:28 -0500
  • f3a57a6b07 Merge pull request #811 from broadinstitute/seru71_fix_MateSameStrandFilter Geraldine Van der Auwera 2015-02-23 17:57:10 -0500
  • 4a493a7900 Update test data so it better reflects the multiallelic AC/AF annotation use case Laura Gauthier 2015-02-20 10:09:33 -0500
  • 9491c0333f Merge pull request #813 from broadinstitute/rhl_throw_exception_dcov jmthibault79 2015-02-19 13:43:32 -0500
  • 2cbaef2fb2 Throw exception for -dcov argument given to ActiveRegionWalkers Ron Levine 2015-02-15 09:04:39 -0500
  • b5f20bbb00 Merge pull request #806 from broadinstitute/ldg_updateNISTinNA12878KB rpoplin 2015-02-17 11:37:44 -0500
  • 72166eee5c Update NA12878KB NIST Genomes-in-a-Bottle from v2.17 to v2.18 Use all sites, not just high confidence Laura Gauthier 2015-01-22 15:32:53 -0500
  • 207f0a69df Merge pull request #809 from broadinstitute/rhl_annotate_strand_allele_counts jmthibault79 2015-02-12 16:33:35 -0500
  • c3ff6df252 StrandAlleleCountsBySample can only be called from HaplotypeCaller Ron Levine 2015-01-30 11:51:45 -0500
  • 3ee0311fdb corrected logical expression in MateSameStrandFilter seru71 2015-02-10 14:11:05 +0100
  • 893e8ff9c4 Merge pull request #810 from broadinstitute/pd_monoallelic_concordance rpoplin 2015-02-10 15:42:40 -0500
  • 92c7c103c1 GenotypeConcordance: monomorphic sites in truth are no longer called "Mismatching Alleles" when the comp genotype has an alternate allele * PT 84700606 Phillip Dexheimer 2015-01-28 22:31:20 -0500
  • b8b23b931e Merge pull request #807 from broadinstitute/rhl_handle_cigar rpoplin 2015-02-01 11:09:52 -0500
  • cf58d671d2 Merge pull request #803 from broadinstitute/pd_toggle_unmapped_scatter pdexheimer 2015-01-31 16:02:15 -0500
  • 3354c07b1c Added optional element "includeUnmapped" to the PartitionBy annotation * The value of this element (default true) determines whether Queue will explicitly run this walker over unmapped reads * This patch fixes a runtime error when FindCoveredIntervals was used with Queue * PT 81777160 Phillip Dexheimer 2015-01-14 21:32:33 -0500
  • d561fc5edc Merge pull request #805 from broadinstitute/ks_gatk_cram rpoplin 2015-01-30 12:55:47 -0500
  • 9d4b876ccd Process X and = CIGAR operators Ron Levine 2015-01-20 12:03:05 -0500
  • 1808c90d2a Added introductory CRAM support. Replaced usage of GATKSamRecordFactory with calls to wrapper GATKSAMRecord extending SAMRecord. Minor other updates for test changes. Added exampleCRAM.cram generated by GATK, with .bai and .crai indexes generated by CRAMTools. CRAM-to-CRAM test disabled due to https://github.com/samtools/htsjdk/issues/148 Using exampleBAM.bam input, outputs of GATK's generated CRAM match CRAMTools generated CRAM, but not samtools/PrintReads SAM output, as things like insert sizes are different. If required for other tools, CRAM indexes must be generated via CRAMTools until we can generate them via CRAMFileWriter. Khalid Shakir 2014-09-23 17:03:15 -0400
  • de3ca65232 Bumping HTSJDK version to pickup a bug fix for CRAM. Khalid Shakir 2015-01-15 13:39:49 -0300
  • e26e55efe1 Merge pull request #802 from broadinstitute/pd_selectvariants_subset Valentin Ruano Rubio 2015-01-22 05:05:42 -0500
  • 72f76add71 Added -trimAlternates argument to SelectVariants * PT 84021222 * -trimAlternates removes all unused alternate alleles from variants. Note that this is pretty aggressive for monomorphic sites Phillip Dexheimer 2014-12-17 22:47:22 -0500
  • d209699485 Merge pull request #804 from broadinstitute/jt_read_filters jmthibault79 2015-01-21 15:45:48 -0500
  • 5ce34d81b8 Allows users to disable specific read filters from the command line - enable this for DuplicateReadFilter only - enable the @DisabledReadFilters annotation to do this at the Walker level Joel Thibault 2014-12-03 15:14:02 -0500
  • 7102477168 Merge pull request #798 from broadinstitute/rhl_split_n_cigar_reads_exception Geraldine Van der Auwera 2015-01-15 00:20:49 -0500
  • 804b2a36b7 Fix SplitNCigar reads exception by making the list of RNAReadTransformer non-abstract, add test for -fixNDN Ron Levine 2015-01-07 09:59:03 -0500
  • 0292d49842 Merge pull request #801 from broadinstitute/pd_gatkvcfconstants rpoplin 2015-01-14 09:43:48 -0500
  • 8599132713 Merge pull request #800 from broadinstitute/ldg_CGPpedError rpoplin 2015-01-14 09:35:33 -0500
  • 6190d660e0 Edits to work with the latest htsjdk release: * TextCigarCodec.decode() is now static, and the getSingleton() method is gone * MergingSamRecordIterator now wants a Collection<SamReader> rather than Collection<SAMFileReader> in the constructor * SeekableBufferedStream now correctly reads the requested number of bytes, removed workaround in GATKBAMIndex Phillip Dexheimer 2015-01-10 14:34:06 -0500
  • b73e9d506a Added GATKVCFConstants and GATKVCFHeaderLines to consolidate the GATK-specific VCF annotations * Removed unused annotations (CCC and HWP) * Renamed one of the two GC annotations to "IGC" (for Interval GC) * Revved picard & htsjdk (GATK constants are now removed from htsjdk) * PT 82046038 Phillip Dexheimer 2014-11-11 22:47:54 -0500
  • 6b2bd5ed09 Address user-reported bug featuring "trio" family with two children, one parent Add test to cover case with family of one parent, two children Laura Gauthier 2015-01-13 16:09:40 -0500
  • cf4ac4a388 Merge pull request #799 from broadinstitute/rp_fix_active_region_downsampling rpoplin 2015-01-09 12:45:58 -0500
  • 2e5f9db758 Raising per-sample limits on the number of reads in ART and HC. Ryan Poplin 2015-01-07 11:32:28 -0500
  • 03203e249e Merge pull request #792 from broadinstitute/rhl_pairhmm_log_stderr rpoplin 2015-01-07 12:41:10 -0500
  • 99ff5fb75b Merge pull request #797 from broadinstitute/vrr_ploidy_limitation_removal rpoplin 2015-01-07 12:38:19 -0500
  • aae04b6122 Fixes explicit limitation of the maximum ploidy of the reference-confidence model Valentin Ruano-Rubio 2015-01-06 13:36:36 -0500
  • 7d58544f17 Do not use logger, write to stderr, could not get the correct logger dependency in pom.xml Ron Levine 2015-01-06 10:32:11 -0500
  • ef32c44688 Merge pull request #795 from broadinstitute/ldg_VQSRcmdlineOutput rpoplin 2015-01-05 14:59:04 -0500
  • 1d5996dd1d Merge pull request #796 from broadinstitute/rp_update_bundle_Axiom_poly rpoplin 2015-01-05 14:53:45 -0500
  • 10b23bfb04 Adding Axiom_Exome_Plus.sites_only.all_populations.poly.vcf to the resource bundle because it is used in the v3.3 best practices Ryan Poplin 2015-01-05 14:52:31 -0500
  • 26c46ae05e Change logger.info to logger.error Ron Levine 2015-01-05 14:14:02 -0500
  • b4fda38922 Use logging system instead of stderr Ron Levine 2015-01-05 14:04:10 -0500
  • e28ee24fc6 Update private single sample pipeline script Laura Gauthier 2015-01-05 12:03:02 -0500
  • 88b6f3aa50 Change []-type arrays to lists so argument parsing works in VCF header commandline output Laura Gauthier 2015-01-05 09:57:56 -0500
  • 3240b3538a Merge pull request #794 from broadinstitute/rhl_read_backed_phasing rpoplin 2015-01-05 09:47:25 -0500
  • 6f566a0e66 Merge pull request #793 from broadinstitute/mf_xhmm_add_genotyping rpoplin 2015-01-05 09:46:06 -0500
  • ac10b9c3cd Merge pull request #791 from broadinstitute/ldg_fixCGPbug rpoplin 2015-01-05 09:40:38 -0500
  • c6840124fe clean up, add final Ron Levine 2015-01-04 23:01:24 -0500
  • 85dc703461 Add TestMergeIntoMNP() and TestReallyMergeIntoMNP() Ron Levine 2015-01-01 09:51:20 -0500
  • bb94833750 Add more tests Ron Levine 2014-12-30 22:45:44 -0500
  • 714d575e3b correct reference file name Ron Levine 2014-12-25 14:00:39 -0500
  • a7fba5c209 restructure and add more tests Ron Levine 2014-12-25 13:57:54 -0500
  • 64375f6341 Messages that were going to stdout now going to stderr Ron Levine 2014-12-20 12:32:06 -0500
  • 11cd0080c3 Add option to genotype additional user-defined interval lists Menachem Fromer 2014-12-21 01:19:03 -0500
  • 069398ad46 Added more tests and documentation Ron Levine 2014-12-19 12:57:43 -0500
  • a9694951d2 Add error handling for genotypes that are called but have no PLs Laura Gauthier 2014-12-18 13:28:56 -0500
  • a4a9e73ec8 Merge pull request #789 from broadinstitute/gg_update_vqsr_example ldgauthier 2014-12-18 13:32:15 -0500
  • b0e615251b Updated VQSR tool docs Geraldine Van der Auwera 2014-12-16 17:26:31 -0500
  • 4a2ac38308 Merge pull request #790 from broadinstitute/rp_nsubtil_fix-snp-detection rpoplin 2014-12-18 09:19:53 -0500
  • 071389b507 Merge pull request #785 from broadinstitute/rhl_variant_multiallelic_annotations rpoplin 2014-12-18 09:11:42 -0500
  • 08790e1dab Fix mmultiallelic info field annotation for VariantAnnotator Ron Levine 2014-12-09 12:44:40 -0500
  • ba949389c5 matchHaplotypeAlleles() no longer calls alleleSegregationIsKnown(), added a TODO to investigate Ron Levine 2014-12-17 14:02:24 -0500
  • d84970ff75 BQSR bug fix from @nsubtil Ryan Poplin 2014-12-17 10:04:26 -0500
  • 56f8e4f9cf Add comments, alleleSegregationIsKnown() check is added to matchHaplotypeAlleles() Ron Levine 2014-12-17 03:25:26 -0500
  • 3deaa4832c Merge pull request #788 from broadinstitute/ldg_fixCombineGVCFsBug Valentin Ruano Rubio 2014-12-16 15:17:33 -0500
  • 011843c569 Fixed huge bug from 9895005a (CombineGVCFs used to stop after the first contig) Laura Gauthier 2014-12-15 10:14:56 -0500
  • bcc6b73e9b Merge pull request #786 from broadinstitute/pd_variantstotable_sma rpoplin 2014-12-16 10:37:22 -0500
  • 3d32babc29 Merge pull request #787 from broadinstitute/vrr_wrong_reference_base_bugfix rpoplin 2014-12-16 10:35:47 -0500
  • 736a857e82 Fixing CombineGVCFs that writes out the wrong REF allele Valentin Ruano-Rubio 2014-12-12 00:01:33 -0500
  • 71bdfbe465 Fix VariantsToTable output of FORMAT record lists when -SMA is specified * PT 84242218 * Note that FORMAT fields behave the same as INFO fields - if the annotation has a count of A (one entry per Alt Allele), it is split across the multiple output lines. Otherwise, the entire list is output with each field Phillip Dexheimer 2014-12-10 21:41:15 -0500
  • b561febbfd Merge pull request #784 from broadinstitute/gg_update_gsalib_version Geraldine Van der Auwera 2014-12-10 13:23:47 -0500
  • 45eddb4ecb Updated gsalib version to 2.1 for resubmitting with updated license to CRAN Geraldine Van der Auwera 2014-12-09 16:19:38 -0500
  • bf2911d62c Merge pull request #783 from broadinstitute/pd_splitsamfile rpoplin 2014-12-08 09:39:03 -0500
  • 5f2a2642d6 Merge pull request #782 from broadinstitute/vrr_gvcf_gq_inconsistency_fix rpoplin 2014-12-08 09:36:23 -0500
  • 385186e11b Makes GQ of Hom-Ref Blocks in GVCF output to be consistent with PLs Valentin Ruano-Rubio 2014-12-04 17:47:56 -0500
  • a5dee8a42e Fix NPE in SplitSamFile * PT 82892316 * Added integration test * Fixed similar error in debug output of HC Phillip Dexheimer 2014-12-04 23:15:09 -0500
  • c9175eeee8 Renamed PhasingUtilitiesUnitTest to PhasingUtilsUnitTest Ron Levine 2014-12-02 18:20:12 -0500
  • bbe78bd181 Merge pull request #779 from broadinstitute/rhl_output_pairhmm rpoplin 2014-12-02 14:30:55 -0500
  • 4e8297360d Merge pull request #780 from broadinstitute/aw_gatkdoclet_fixes rpoplin 2014-12-02 10:57:57 -0500
  • b8f0f3fdd2 Add argument for loading the vector HMM library once Ron Levine 2014-11-26 15:59:02 -0500
  • 4fe6ccec98 Add -output-file-extension option to GATKDoclet to produce html instead of php. Alec Wysoker 2014-12-01 17:47:17 -0500
  • 62e5d42380 Fix code to filter current directory from paths pass to Reflection library. Alec Wysoker 2014-12-01 17:45:46 -0500
  • 2fa8fe2415 Merge pull request #777 from broadinstitute/rhl_specify_pairhmm droazen 2014-11-26 11:34:51 -0500
  • 386aeda022 Add HaplotypeCaller argument so integration tests can specify the hardware dependent PairHMM sub-implementation Ron Levine 2014-11-14 11:30:47 -0500
  • 34241a62f6 Use a publicly accessible sequence file Ron Levine 2014-11-24 11:18:21 -0500
  • 6ff698c556 Added HP and non-HP tests for matchHaplotypeAlleles(), added a nominal test for mergeIntoMNPvalidationCheck() Ron Levine 2014-11-24 11:08:04 -0500