e1862a04a8
Merge pull request #862 from broadinstitute/rhl_doc_args_incompatibility
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Log a warning if using incompatible arguments in DepthOfCoverage
2015-03-11 13:08:53 -04:00
bee7f655b7
Log a warning if using incompatible arguments in DepthOfCoverage
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Add reference gene list file
2015-03-10 18:14:21 -04:00
6645669eca
Merge pull request #818 from broadinstitute/mf_CheckNameInAssessNA12878
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Mf check name in assess na12878
2015-03-10 10:33:05 -04:00
957946c73c
Change to AssessNA12878 to allow for analysis of files that specify name differing from NA12878.
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Added an integration test to test the sampleNameToCompare option, and a VCF file for this test to run on.
2015-03-10 10:15:02 -04:00
4bff024107
Merge pull request #819 from broadinstitute/rhl_fix_docs_npa_filter
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Fix NotPrimaryAlignmentFilter documentation
2015-03-06 07:46:33 -05:00
71d68c3d93
Fix NotPrimaryAlignmentFilter documentation
2015-03-05 20:30:46 -05:00
f8f2680142
Merge pull request #812 from broadinstitute/ldg_combineData_submit
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New walker to combine WGS and WES data
2015-03-02 15:12:31 -05:00
83bd85d8de
Merge pull request #817 from broadinstitute/ldg_fixQueueTests
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Change UG @PartitionBy to fix Queue tests
2015-03-02 09:49:17 -05:00
aaf952469e
Change UG @PartitionBy to fix Queue tests
2015-03-01 14:42:43 -05:00
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)
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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
2015-03-01 12:44:32 -05:00
2d992ad818
Modify assessment/site reporting criteria for better bookkeeping
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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
2015-03-01 12:44:32 -05:00
8efaa97d84
Merge pull request #815 from broadinstitute/ldg_updateMulitallelicVAtestData
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Update test data so it better reflects the multiallelic AC/AF annotation...
2015-03-01 12:10:25 -05:00
21390575dd
Merge pull request #816 from broadinstitute/rhl_gc_content_value_type
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Change GC Content value type from Integer to Float
2015-02-26 15:26:28 -05:00
44e5965a4b
Change GC Content value type from Integer to Float
2015-02-25 13:56:42 -05:00
f3a57a6b07
Merge pull request #811 from broadinstitute/seru71_fix_MateSameStrandFilter
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Corrected logical expression in MateSameStrandFilter
2015-02-23 17:57:10 -05:00
4a493a7900
Update test data so it better reflects the multiallelic AC/AF annotation use case
2015-02-20 19:02:42 -05:00
9491c0333f
Merge pull request #813 from broadinstitute/rhl_throw_exception_dcov
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Throw exception for -dcov argument given to ActiveRegionWalkers
2015-02-19 13:43:32 -05:00
2cbaef2fb2
Throw exception for -dcov argument given to ActiveRegionWalkers
2015-02-19 08:24:39 -05:00
b5f20bbb00
Merge pull request #806 from broadinstitute/ldg_updateNISTinNA12878KB
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Update NA12878KB NIST Genomes-in-a-Bottle from v2.17 to v2.18
2015-02-17 11:37:44 -05:00
72166eee5c
Update NA12878KB NIST Genomes-in-a-Bottle from v2.17 to v2.18
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Use all sites, not just high confidence
2015-02-17 08:17:57 -05:00
207f0a69df
Merge pull request #809 from broadinstitute/rhl_annotate_strand_allele_counts
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StrandAlleleCountsBySample can only be called from HaplotypeCaller
2015-02-12 16:33:35 -05:00
c3ff6df252
StrandAlleleCountsBySample can only be called from HaplotypeCaller
2015-02-12 13:43:48 -05:00
3ee0311fdb
corrected logical expression in MateSameStrandFilter
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Signed-off-by: David Roazen <droazen@broadinstitute.org>
2015-02-12 12:21:44 -05:00
893e8ff9c4
Merge pull request #810 from broadinstitute/pd_monoallelic_concordance
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GenotypeConcordance: monomorphic sites in truth are no longer...
2015-02-10 15:42:40 -05:00
92c7c103c1
GenotypeConcordance: monomorphic sites in truth are no longer called "Mismatching Alleles" when the comp genotype has an alternate allele
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* PT 84700606
2015-02-07 15:54:38 -05:00
b8b23b931e
Merge pull request #807 from broadinstitute/rhl_handle_cigar
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Process X and = CIGAR operators
2015-02-01 11:09:52 -05:00
cf58d671d2
Merge pull request #803 from broadinstitute/pd_toggle_unmapped_scatter
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Added optional element "includeUnmapped" to the PartitionBy annotation
2015-01-31 16:02:15 -05:00
3354c07b1c
Added optional element "includeUnmapped" to the PartitionBy annotation
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* 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
2015-01-31 15:47:57 -05:00
d561fc5edc
Merge pull request #805 from broadinstitute/ks_gatk_cram
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Introductory GATK CRAM support
2015-01-30 12:55:47 -05:00
9d4b876ccd
Process X and = CIGAR operators
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Add simple BaseRecalibrator integration test for CIGAR = and X operators
2015-01-29 17:00:00 -05:00
1808c90d2a
Added introductory CRAM support.
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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.
Generation of exampleCRAM.cram:
* java -jar target/executable/GenomeAnalysisTK.jar -T PrintReads -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I public/gatk-utils/src/test/resources/exampleBAM.bam -o public/gatk-utils/src/test/resources/exampleCRAM.cram
* java -jar cramtools-2.1.jar index -I public/gatk-utils/src/test/resources/exampleCRAM.cram
* java -jar cramtools-2.1.jar index -I public/gatk-utils/src/test/resources/exampleCRAM.cram --bam-style-index
CRAM generation by existing tools:
* samtools view -C -T public/gatk-utils/src/test/resources/exampleFASTA.fasta -o testSamtools.cram public/gatk-utils/src/test/resources/exampleBAM.bam
* java -jar cramtools-2.1.jar cram --ignore-md5-mismatch --capture-all-tags -Q -n -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I public/gatk-utils/src/test/resources/exampleBAM.bam -O testCRAMTools.cram
* java -jar target/executable/GenomeAnalysisTK.jar -T PrintReads -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I public/gatk-utils/src/test/resources/exampleBAM.bam -o testGATK.cram
CRAMTools view of the above:
* java -jar cramtools-2.1.jar bam --skip-md5-check -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I public/gatk-utils/src/test/resources/exampleCRAM.cram | tail -n 1
* java -jar cramtools-2.1.jar bam --skip-md5-check -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I testSamtools.cram | tail -n 1
* java -jar cramtools-2.1.jar bam --skip-md5-check -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I testCRAMTools.cram | tail -n 1
* java -jar cramtools-2.1.jar bam --skip-md5-check -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I testGATK.cram | tail -n 1
2015-01-26 14:47:39 -03:00
de3ca65232
Bumping HTSJDK version to pickup a bug fix for CRAM.
2015-01-26 14:47:39 -03:00
e26e55efe1
Merge pull request #802 from broadinstitute/pd_selectvariants_subset
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Added -trimAlternates argument to SelectVariants
2015-01-22 05:05:42 -05:00
72f76add71
Added -trimAlternates argument to SelectVariants
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* PT 84021222
* -trimAlternates removes all unused alternate alleles from variants. Note that this is pretty aggressive for monomorphic sites
2015-01-21 21:33:35 -05:00
d209699485
Merge pull request #804 from broadinstitute/jt_read_filters
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Allows users to disable the DuplicateReadFilter
2015-01-21 15:45:48 -05:00
5ce34d81b8
Allows users to disable specific read filters from the command line
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- enable this for DuplicateReadFilter only
- enable the @DisabledReadFilters annotation to do this at the Walker level
2015-01-21 13:17:29 -05:00
7102477168
Merge pull request #798 from broadinstitute/rhl_split_n_cigar_reads_exception
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Rhl split n cigar reads exception
2015-01-15 00:20:49 -05:00
804b2a36b7
Fix SplitNCigar reads exception by making the list of RNAReadTransformer non-abstract, add test for -fixNDN
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Includes documentation changes for -fixNDN argument and the read transformer documentation.
Documentation changes to CombineVariants
2015-01-14 22:22:05 -05:00
0292d49842
Merge pull request #801 from broadinstitute/pd_gatkvcfconstants
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Collected VCF IDs and header lines into one place
2015-01-14 09:43:48 -05:00
8599132713
Merge pull request #800 from broadinstitute/ldg_CGPpedError
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Address user-reported bug featuring "trio" family with two children, one...
2015-01-14 09:35:33 -05:00
6190d660e0
Edits to work with the latest htsjdk release:
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* 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
2015-01-13 21:32:10 -05:00
b73e9d506a
Added GATKVCFConstants and GATKVCFHeaderLines to consolidate the GATK-specific VCF annotations
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* 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
2015-01-13 21:32:09 -05:00
6b2bd5ed09
Address user-reported bug featuring "trio" family with two children, one parent
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Add test to cover case with family of one parent, two children
2015-01-13 18:35:44 -05:00
cf4ac4a388
Merge pull request #799 from broadinstitute/rp_fix_active_region_downsampling
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Raising per-sample limits on the number of reads in ART and HC.
2015-01-09 12:45:58 -05:00
2e5f9db758
Raising per-sample limits on the number of reads in ART and HC.
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-- Active Region Traversal was using per sample limits on the number of reads that were too low, especially now that we are running one sample at a time. This caused issues with high confidence variants being dropped in high coverage data.
-- HaplotypeCallerGVCFIntegrationTest PL/annotation changes due to using more reads in those tests
-- Removed a CountReadsInActiveRegionsIntegrationTest test for excessive coverage because the read coverage no longer goes over the limits in ART
2015-01-09 11:21:42 -05:00
03203e249e
Merge pull request #792 from broadinstitute/rhl_pairhmm_log_stderr
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Rhl pairhmm log stderr
2015-01-07 12:41:10 -05:00
99ff5fb75b
Merge pull request #797 from broadinstitute/vrr_ploidy_limitation_removal
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MERGE AFTER TEST PASS: Fixes explicit limitation of the maximum ploidy of the reference-confide...
2015-01-07 12:38:19 -05:00
aae04b6122
Fixes explicit limitation of the maximum ploidy of the reference-confidence model
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Story:
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- https://www.pivotaltracker.com/story/show/83803796
Changes:
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- From a fix maximum ploidy indel RCM likelihood cache to a
dynamically resizable one.
- Used the occassion to removed an unused and deprecated method from ReferenceConfidenceModel
Testing:
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- Added integration test to check on ploidies larger than the previous limit of 20.
2015-01-07 10:43:22 -05:00
7d58544f17
Do not use logger, write to stderr, could not get the correct logger dependency in pom.xml
2015-01-06 10:32:11 -05:00
ef32c44688
Merge pull request #795 from broadinstitute/ldg_VQSRcmdlineOutput
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VQSR VCF header command line now contains annotations and tranche levels
2015-01-05 14:59:04 -05:00
Geraldine Van der Auwera
Ron Levine
ldgauthier
Mark Fleharty
Valentin Ruano Rubio
jmthibault79
rpoplin
seru71
Phillip Dexheimer
rpoplin
pdexheimer
Khalid Shakir