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
1d5996dd1d
Merge pull request #796 from broadinstitute/rp_update_bundle_Axiom_poly
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Adding Axiom_Exome_Plus.sites_only.all_populations.poly.vcf to the resou...
2015-01-05 14:53:45 -05:00
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
2015-01-05 14:52:31 -05:00
26c46ae05e
Change logger.info to logger.error
2015-01-05 14:14:02 -05:00
b4fda38922
Use logging system instead of stderr
2015-01-05 14:04:10 -05:00
e28ee24fc6
Update private single sample pipeline script
2015-01-05 12:11:21 -05:00
88b6f3aa50
Change []-type arrays to lists so argument parsing works in VCF header commandline output
2015-01-05 10:21:06 -05:00
3240b3538a
Merge pull request #794 from broadinstitute/rhl_read_backed_phasing
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Rhl read backed phasing
2015-01-05 09:47:25 -05:00
6f566a0e66
Merge pull request #793 from broadinstitute/mf_xhmm_add_genotyping
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Add option to genotype additional user-defined interval lists
2015-01-05 09:46:06 -05:00
ac10b9c3cd
Merge pull request #791 from broadinstitute/ldg_fixCGPbug
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Add error handling for genotypes that are called but have no PLs
2015-01-05 09:40:38 -05:00
c6840124fe
clean up, add final
2015-01-04 23:01:24 -05:00
85dc703461
Add TestMergeIntoMNP() and TestReallyMergeIntoMNP()
2015-01-01 09:51:20 -05:00
bb94833750
Add more tests
2014-12-30 22:45:44 -05:00
714d575e3b
correct reference file name
2014-12-25 14:00:39 -05:00
a7fba5c209
restructure and add more tests
2014-12-25 13:57:54 -05:00
64375f6341
Messages that were going to stdout now going to stderr
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Make PairHMM outputs go to stderr instead of stdout
Change output from stdout to stderr in close()
Updated lib with output going to stderr
2014-12-23 11:03:29 -05:00
11cd0080c3
Add option to genotype additional user-defined interval lists
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Add Qscript 'ONLY_GENOTYPE_xhmmCNVpipeline' to genotype additional user-defined interval lists
Add Qscript 'ONLY_GENOTYPE_xhmmCNVpipeline' to genotype additional user-defined interval lists (and similar option to Qscript 'xhmmCNVpipeline')
2014-12-21 13:02:17 -05:00
069398ad46
Added more tests and documentation
2014-12-19 12:57:43 -05:00
a9694951d2
Add error handling for genotypes that are called but have no PLs
2014-12-18 15:03:20 -05:00
a4a9e73ec8
Merge pull request #789 from broadinstitute/gg_update_vqsr_example
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Updated VQSR tool docs
2014-12-18 13:32:15 -05:00
b0e615251b
Updated VQSR tool docs
2014-12-18 12:59:37 -05:00
4a2ac38308
Merge pull request #790 from broadinstitute/rp_nsubtil_fix-snp-detection
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BQSR bug fix from @nsubtil
2014-12-18 09:19:53 -05:00
071389b507
Merge pull request #785 from broadinstitute/rhl_variant_multiallelic_annotations
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Rhl variant multiallelic annotations
2014-12-18 09:11:42 -05:00
08790e1dab
Fix mmultiallelic info field annotation for VariantAnnotator
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Add multi-allele test for info field annotations
Fix to process all types of INFO annotations
roll back to previous version, removes INFO and FORMAT
Correct @return for VariantAnnotatorEngine.getNonReferenceAlleles()
Enhance comments and clean up multi-allelic logic, handle header info number = R
only parse counts of A & R
Add INFO for AC
update MD5
Performance enhancement, only parse multiallelic with a count A or R
Make argument final in getNonReferenceAlleles()
Code cleanup, add exceptions for bad expression/allele size mismatch and missing header info for an expression
Change exception to warning for expression value/number of alleles check
remove adevertised exceptions
2014-12-17 22:21:00 -05:00
ba949389c5
matchHaplotypeAlleles() no longer calls alleleSegregationIsKnown(), added a TODO to investigate
2014-12-17 14:02:24 -05:00
d84970ff75
BQSR bug fix from @nsubtil
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-- Ignore SNP matches that lie outside the clipped read window
-- This fixes an issue where GATK would skip the entire read if a SNP is entirely
contained within a sequencing adapter.
2014-12-17 10:04:37 -05:00
rpoplin
pdexheimer
Phillip Dexheimer
Ron Levine
Khalid Shakir
Valentin Ruano Rubio
jmthibault79
Geraldine Van der Auwera
Laura Gauthier
Menachem Fromer