31e58ae4ecRefactored AFCalc to remove unecessary capability limits allowing to deal with mixed ploidies and max-alt-allele number changes dynamically.
Valentin Ruano-Rubio
2014-09-10 12:51:39 -0400
7f6e526a87Merge pull request #732 from broadinstitute/rp_ignore_all_filters_in_VQSR
Eric Banks
2014-09-12 00:17:20 -0400
48252897b4Added ignore all filters options to VQSR walkers
Ryan Poplin
2014-09-10 13:34:04 -0400
31cea25c36Merge pull request #730 from broadinstitute/eb_inbreeding_coeff_unit_test
Eric Banks
2014-09-10 09:32:49 -0400
5e490362caCleaned up and fleshed out unit tests for the Inbreeding Coefficient annotation class.
Eric Banks
2014-09-08 11:40:39 -0400
78a61dc3e8Merge pull request #729 from broadinstitute/eb_improve_dangling_head_merging_PT74221002
Eric Banks
2014-09-08 10:28:51 -0400
cc175bad40Improve the accuracy of dangling head merging in the HC assembler.
Eric Banks
2014-09-02 12:42:13 -0400
56a2554bb0Merge pull request #720 from broadinstitute/pd_standardize_args
Eric Banks
2014-09-06 20:49:58 -0400
a35f5b8685Moved arguments controlling options in output files into the engine * Arguments involved are --no_cmdline_in_header, --sites_only, and --bcf for VCF files and --bam_compression, --simplifyBAM, --disable_bam_indexing, and --generate_md5 for BAM files * PT 52740563 * Removed ReadUtils.createSAMFileWriterWithCompression(), replaced with ReadUtils.createSAMFileWriter(), which applies all appropriate engine-level arguments * Replaced hard-coded field names in ArgumentDefinitionField (Queue extension generator) with a Reflections-based lookup that will fail noisily during extension generation if there's an error
Phillip Dexheimer
2014-08-26 21:46:30 -0400
5c4a3eb89cMerge pull request #727 from broadinstitute/ks_gatk_queue_package_test_updates
droazen
2014-09-05 10:17:32 -0400
0c336e0eb8Merge pull request #728 from broadinstitute/rp_SOR_standard_annotation
Eric Banks
2014-09-05 10:06:52 -0400
a45acdfb89StrandOddsRatio is now a standard annotation.
Ryan Poplin
2014-09-04 13:57:14 -0400
376592f423Various fixes for package tests. Explicitly including gatk/queue test-jar artifacts in package test classpaths. SelectVariantsIntegrationTest#testInvalidJexl now resets the JexlEngine silent flag that VariantFiltration.initialize() toggles. External example no longer tries to unpack nonexistent gatk artifact jars during package tests.
Khalid Shakir
2014-08-31 12:35:53 -0400
9705df2f7aMerge pull request #726 from broadinstitute/rp_haplotypeCaller_typo_fix
rpoplin
2014-09-04 15:04:41 -0400
1b809268d5fixing a few small typos in the HaplotypeCaller and related classes
Ryan Poplin
2014-09-04 14:48:27 -0400
f53ea3b456Merge pull request #725 from broadinstitute/ks_remove_ipflibrary_symlink
kshakir
2014-09-04 22:14:02 +0800
f7c37eff06Fixed old symlink reference in IPFLibraryQueueTest.
Khalid Shakir
2014-09-04 22:13:17 +0800
5c087a6e1fMerge pull request #724 from broadinstitute/ks_remove_test_qscript_symbolic_links
droazen
2014-09-04 09:10:54 -0400
538537dbf1Merge pull request #718 from broadinstitute/mf_rbp_fix
Eric Banks
2014-09-02 20:39:22 -0400
01e725cd1aMerge pull request #723 from broadinstitute/eb_fix_rna_splitting_PT77878554
Eric Banks
2014-09-02 20:39:01 -0400
10f9001738Fix MNP merging code to work with explicit HP phase representation
Menachem Fromer
2014-08-27 14:06:28 -0400
ff91ab8ba2Make sure that the OverhangFixingManager (used for splitting RNA reads) handles unmapped reads.
Eric Banks
2014-09-01 12:53:37 -0400
d363725b4bAdds support for omniploidy to GenotypeGVCFs and CombineGVCFs.
Valentin Ruano-Rubio
2014-08-27 14:43:20 -0400
fe86dafc41Merge pull request #705 from broadinstitute/gg_simplify_gatkdocs_templates
Eric Banks
2014-09-02 06:28:26 -0400
fcb0eca203Now passing in the path to the GATK directory to tests. Changed tests and scripts to use gatkdir full path instead of relative testdata/qscripts symbolic links. Although symlinks not created, left the symlink deletion script execution with a comment about future removal. Re-enabled example UG pipeline queue test. Replaced all hardcoded strings of {public,private}/testdata with BaseTest variables. Refactored temp list creation method from ListFileUtilsUnitTest to BaseTest.createTempListFile. Removed list files with hardcoded paths, now using createTempListFile instead with private test dir variable.
Khalid Shakir
2014-09-01 18:15:19 +0800
9477a6ab1aMerge pull request #722 from broadinstitute/ks_mlinderm_taggable_RodBindingCollection
kshakir
2014-09-01 18:07:07 +0800
380cd67146Update extension generator to recognize RodBindingCollection as 'taggable'
Michael Linderman
2014-08-18 18:54:26 -0400
46b0c18603Merge pull request #721 from broadinstitute/ks_save_analyze_covariates_integration_test_inputs
Eric Banks
2014-08-29 18:44:40 -0400
2d28972c88The 'after' files are @Input files and commited in git, so don't delete them after tests.
Khalid Shakir
2014-08-30 03:04:54 +0800
b654590ed6Merge pull request #717 from broadinstitute/eb_change_phasing_of_hom_vars
Eric Banks
2014-08-25 21:41:11 -0400
5b087c9897Changed the functionality of the physical phasing in the HC: now hom vars are output as 0|1.
Eric Banks
2014-08-25 11:57:30 -0400
6dc5cf0be0Fixes some missmerged md5 updates from a previous merge into master
Valentin Ruano-Rubio
2014-08-24 20:47:07 -0400
9009c1e996Merge pull request #715 from broadinstitute/vrr_disable_physical_phasing_for_nondiploid_hc
Eric Banks
2014-08-23 20:58:51 -0400
34e5cce553Merge pull request #714 from broadinstitute/pd_hc_samplename
Eric Banks
2014-08-23 20:57:44 -0400
6695aeafd9Disable physical phasing for non-diploid HC calling.
Valentin Ruano-Rubio
2014-08-22 11:26:17 -0400
931890915fAdd the --sample_name argument to HaplotypeCaller * This is a shortcut for people who have multi-sample BAMs but would like to use GVCF mode. Rather than creating single-sample BAMs with PrintReads, one could use the --sample_name argument to HaplotypeCaller to specify the single sample to make calls on * Completes PT 73075482
Phillip Dexheimer
2014-08-08 08:26:22 -0400
fc5ce4b662Created the stand-alone AC and AF annotation AlleleCountBySample
Valentin Ruano-Rubio
2014-08-20 13:58:52 -0400
36bdfa3918Merge pull request #712 from broadinstitute/eb_physical_phasing_bug_PT77248992
Eric Banks
2014-08-21 15:25:51 -0400
b1cb6196beFixing bug in the physical phasing code, found by Valentin.
Eric Banks
2014-08-20 09:24:47 -0400
e60dd77362Merge pull request #711 from broadinstitute/ldg_deNovoAnnotation
rpoplin
2014-08-21 15:06:42 -0400
9a5da41dd4Add bells and whistles for Genotype Refinement Pipeline New annotation for low= and high-confidence de novos (only annotates biallelics) FamilyLikelihoodsUtils now add joint likelihood and joint posterior annotations Restrict population priors based on discovered allele count to be valid for 10 or more samples.
Laura Gauthier
2014-07-21 15:17:01 -0400
d31c5536aaFixed the bug first by indicating the actual possible number of alternatives alleles considering the extra <NON_REF> and second by resizing the StateTracker capacity when invoked by GeneralPloidyExactAFCalc deep within its implementation of computeLog10PNonRef which is ultimatelly what get rids of the exception.
Valentin Ruano-Rubio
2014-08-19 11:44:24 -0400
78c2da1fefMerge pull request #708 from broadinstitute/ldg_SBannotationWarnings
Eric Banks
2014-08-20 09:30:06 -0400
b512c7eac9Refactor StrandBiasTest (using template method) and add warnings for when annotations may not be calculated successfully. VariantAnnotator/FS behavior changes slightly: VA used to output zeros for FS if there was no strand bias info, now skips FS output (but will still show FS in header)
Laura Gauthier
2014-08-18 14:44:26 -0400
8d9a55ae60Moving new omniploidy likelihood calculation classes to their final package (as far as this pull-request is concerned) in org.broadinstitute.gatk.tools.walkers.genotyper
Valentin Ruano-Rubio
2014-08-19 10:32:02 -0400
611b7f25eaAdds unit-test and integration test for new omniploidy likelihood calculation components Added md5 to HaplotypeCallerIntegrationTest.testHaplotypeCallerSingleSampleWithDbsnp
Valentin Ruano-Rubio
2014-08-13 14:06:52 -0400
9ee9da36bbGeneralize the calculation of the genotype likelihoods in HC to cope with haploid and multiploidy Changes in several walker to use new sample, allele closed lists and new GenotypingEngine constructors signatures
Valentin Ruano-Rubio
2014-08-18 15:29:28 -0400
f08dcbc160Added the genotype likelihoods model interface and implementation for the random speciment sample from an infinite population with homogeneous ploidy accross samples.
Valentin Ruano-Rubio
2014-08-18 15:28:27 -0400
4f993e8dbeAdded read-likelihoods array base structure to substitute existing Map-of-Map-of-Maps.
Valentin Ruano-Rubio
2014-08-12 18:04:43 -0400
242cd0e58fAdded genotype allele counts and likelihood calculator utilities for arbitrary ploidy and number of alleles
Valentin Ruano-Rubio
2014-06-04 01:36:52 -0400
b0a4cb9f0cAdded close sample and allele list data-structures and utility classes
Valentin Ruano-Rubio
2014-06-04 01:33:29 -0400
cdba069b02changed the GATKDocs format to PHP
Geraldine Van der Auwera
2014-08-15 01:04:26 -0400
1af78f707eMerge pull request #707 from broadinstitute/eb_improve_physical_phasing
Eric Banks
2014-08-18 16:27:40 -0400
d3f06024f8Updated the physical phasing in the Haplotype Caller to address requests from ATGU.
Eric Banks
2014-08-15 17:47:32 -0400
7e0c326e1cMerge pull request #706 from broadinstitute/vrr_reduce_hc_integration_test_time
Eric Banks
2014-08-15 17:37:57 -0400
cab02f8401Merge pull request #703 from broadinstitute/eb_keep_original_ac_for_multiallelics
Eric Banks
2014-08-15 17:36:32 -0400
2f79042deeReduce intervals of integration tests in HaplotypeCallerIntegrationTest class
Valentin Ruano-Rubio
2014-08-15 11:29:53 -0400
eb84091702Update the --keepOriginalAC functionality in SelectVariants to work for sites that lose alleles in the selection.
Eric Banks
2014-08-14 12:57:17 -0400
20f72e1d0cMerge pull request #702 from broadinstitute/rp_fix_genotypeGVCFs_AD_ordering
Ryan Poplin
2014-08-13 15:00:48 -0400
3a9a78c785Removing an assumption that ADs were in the same order if the number of alleles matched. This happens for example when one sample is C->T and another sample is C->G.
Ryan Poplin
2014-08-13 10:28:12 -0400
c6a96c3958Merge pull request #688 from broadinstitute/ks_na12878kb_utils_sting_to_gatk_updates
Eric Banks
2014-08-13 12:30:54 -0400
27193c5048Merge pull request #700 from broadinstitute/eb_phase_HC_variants_PT74816060
Eric Banks
2014-08-13 12:30:32 -0400
4512940e87Initial implementation of functionality to add physical phasing information to the output of the HaplotypeCaller.
Eric Banks
2014-07-14 14:57:56 -0400
149f98e28aMerge pull request #701 from broadinstitute/gg_amend_ET_doc_76823436
Eric Banks
2014-08-12 17:40:46 -0400
49702dc695Clarified Phone Home system details re: privacy
Geraldine Van der Auwera
2014-08-12 17:23:35 -0400
6d7201a7f8Merge pull request #698 from broadinstitute/pd_printreads_subset
jmthibault79
2014-08-12 14:13:07 -0400
7e77875c81Improvements to read-group filtering in PrintReads - Read groups that are excluded by sample_name, platform, or read_group arguments no longer appear in the header - The performance penalty associated with filtering by read group has been essentially eliminated - Partial fulfillment of PT 73075482
Phillip Dexheimer
2014-08-06 22:17:22 -0400
b39508cd15ReadLikelihoods class introduction final changes before merging
Valentin Ruano-Rubio
2014-08-11 17:47:25 -0400
9a9a68409eReadLikelihoods class introduction final changes before merging
Valentin Ruano-Rubio
2014-07-31 15:47:46 -0400
0b472f6bffAdded new test to verify the functionality of ReadLikelihoods.java and its use in HC. Updated existing integration test md5s.
Valentin Ruano-Rubio
2014-08-07 17:05:08 -0400
2914ecb585Change the Map-of-maps-of-maps for an array based implementation ReadLikelihoods to hold read likelihoods.
Valentin Ruano-Rubio
2014-08-07 17:03:12 -0400
09ac3779d6Added ReadLikelihoods component to substitute Map<String,PerReadAlleleLikelihoodMap>. It uses a more efficient java array[] based implementation and encapsulates operations perform with such a read-likelihood collection such as marginalization, filtering by position, poor modeling or capping worst likelihoods and so forth.
Valentin Ruano-Rubio
2014-07-24 23:42:53 -0400
c56e493f98Merge pull request #622 from broadinstitute/ldg_SORanalysis
Ryan Poplin
2014-08-11 09:45:27 -0400
abcaba4bc3Merge pull request #699 from broadinstitute/tf_hc_block_ranges
Eric Banks
2014-08-08 16:10:23 -0400
5695f22da8Changed the default GVCF Q Bands from 5,20,60 to be 1..60 by 1s, 60...90 by 10s and 99 in order to give finer resolution for homref PLs and ADs at lower confidences and somewhat higher resolution at higher confidences.
Tim Fennell
2014-08-07 10:43:09 -0400
35de598e4bModify StrandOddsRatio calculation to take on lower values in cases where reference +/- reads are skewed but alt reads are not. Add SOR to default annotations produced by GenotypeGVCFs. Add jitter to minimum SOR values
Laura Gauthier
2014-04-15 15:35:45 -0400
683baff375Merge pull request #697 from broadinstitute/ldg_inbreedingCoeffForMultiallelics
ldgauthier
2014-08-07 11:57:39 -0400
f532f1f843Fix nullPointerException
Laura Gauthier
2014-08-07 10:00:14 -0400
0b72f7a16dMerge pull request #685 from broadinstitute/ldg_inbreedingCoeffForMultiallelics
Eric Banks
2014-08-07 09:00:09 -0400
74affcc077Update inbreeding coefficient calculation to give a better estimate for multialleleic sites Add unit test for compound het and for multiallelic hets
Laura Gauthier
2014-07-09 15:36:09 -0400
b9486f5b4dMerge pull request #693 from broadinstitute/ldg_SORfromHC
Eric Banks
2014-08-06 21:48:09 -0400
5f31e54d67Merge pull request #696 from broadinstitute/pd_DoC_sorting
Eric Banks
2014-08-06 08:35:35 -0400
6fa4764fc1Merge pull request #694 from broadinstitute/pd_check_missing_arg_values
Eric Banks
2014-08-06 08:32:22 -0400
b0c026e671Fix sample sort order bug in DepthOfCoverage Rare bug triggered by hash collision between sample names PT 66183936
Phillip Dexheimer
2014-08-05 21:55:34 -0400
593663d9b6Improved detection of missing argument values In particular, it was possible to specify arguments for Files or Compound types without values Added a special "none" value for annotations, since a bare "-A" is no longer allowed Delivers PT 71792842 and 59360374
Phillip Dexheimer
2014-07-07 22:48:53 -0400
03e7ee6e9cMerge pull request #695 from broadinstitute/pd_genotype_concordance_doc
Eric Banks
2014-08-05 07:15:40 -0400
359fe150c9Documentation fix (closed HTML tag)
Phillip Dexheimer
2014-08-04 23:19:16 -0400
5533199402Allow SOR to be calculated from HC Refactor StrandBiasTest classes
Laura Gauthier
2014-08-01 13:55:06 -0400
e69b0d6316Merge pull request #692 from broadinstitute/rp_typo_analyze_covariates
Ryan Poplin
2014-07-31 10:39:31 -0400
63b3f7dfd3Fixing typos in AnalyzeCovariates
Ryan Poplin
2014-07-31 10:36:18 -0400
66ccc636b8Merge pull request #691 from broadinstitute/ldg_update_htsjdk
Eric Banks
2014-07-30 14:32:23 -0400
4373922ee6Update GATK to work with latest htsjdk ValidationStringency was moved from htsjdk.samtools.SAMFileReader to htsjdk.samtools samtools find BAM index file method was also moved (and made public!)
Laura Gauthier
2014-07-29 09:09:55 -0400
Valentin Ruano-Rubio
Eric Banks
Ryan Poplin
Phillip Dexheimer
droazen
Khalid Shakir
kshakir
Menachem Fromer
Michael Linderman
Laura Gauthier
Geraldine Van der Auwera
jmthibault79
Tim Fennell