61875e4dfa
Fix LeftAlignAndTrimVariants -split to not change no-call genotypes to hom-ref
2017-02-22 17:57:59 -05:00
3c347c1385
Total ploidy does not have to equal to the number of priors
2017-02-20 20:28:41 -05:00
1d36d9fd69
Move htsjdk to ver 2.9.0 and picard to ver 2.8.3
2017-02-17 07:03:03 -05:00
dce2e29ade
Change ALLOW_N_CIGARS to ALLOW_N_CIGAR_READS in doc
2017-01-18 15:11:52 -05:00
7c0e51396f
Merge pull request #1539 from broadinstitute/rhl_hc_disable_badmatefilter_1443
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Allow disabling of BadMateFilter in HaplotypeCaller
2017-01-18 12:39:22 -05:00
1f6645539a
Make upstreamDeletionsLoc ThreadLocal
2017-01-12 14:09:24 -05:00
f092e1438d
Allow disabling of BadMateFilter in HaplotypeCaller
2017-01-11 14:49:45 -05:00
44c0609418
Log annotation warning once if using multithreads
2017-01-08 09:58:40 -05:00
4f52395795
Synchronize modification/access to practicalAlleleCountForPloidy
2017-01-06 22:16:35 -05:00
ab4a9fa64f
Update stand_call_conf doc strings
2017-01-06 17:15:56 -05:00
e86da63d04
Update pom versions to mark the start of GATK 3.8 development
2016-12-12 08:53:23 -05:00
56f2c1ac75
Update pom versions for the 3.7 release
2016-12-12 08:49:43 -05:00
5602095a24
Move htsjdk to ver 2.8.1 and picard to ver 2.7.2
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- Updating VF and tests to match new jexl behavior from htsjdk
- Use Z instead of DP to test behavior on missing annotation
2016-12-10 11:50:30 -05:00
1291cfa881
Merge pull request #1529 from broadinstitute/ms_fs
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Make Fisher Exact Test match R and GATK4 p-values
2016-12-06 08:55:08 -05:00
172db666d6
Output files with the vcf.gz extension are gzipped, containing .bcf not as an extension result in VCF"
2016-12-05 22:25:59 -05:00
234ccdf0c3
Merge pull request #1496 from broadinstitute/db_m2_downsampling
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Expose downsampling parameters as CLI arguments to Mutect2
2016-12-05 21:53:25 -05:00
3265a664c4
Makes Fisher's exact test match R and GATK4
2016-12-05 16:46:47 -05:00
b1f2301dd3
Add downsampling arguments to Mutect
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- maxReadsInRegionPErSample, minReadsPerAlignment start are now M2 args
- maxReadsInMemoryPerSample is an activeRegionWalker arg
2016-12-05 14:12:22 -05:00
b42dc1624b
Documentation fixes
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- Fix missing closing code block tag
- SOR fix + minor fix to template
- Minor typo fixes
- Make no_cmdline_in_header arg visible in docs
- Caveats for UG-only args that are difficult to move out of common collection
- Reference -L and -XL in -gvcf documentation
- Annotation doc fixes (dsde-docs#1289)
- Unhide some ContEst args and make Advanced
- Fix inputPrior error message
- Update web urls
- Add JEXL doc link
2016-12-05 14:09:44 -05:00
68b6f8f638
Replace VariantContextWriterFactory with VariantContextWriterBuilder
2016-11-30 16:04:25 -05:00
055d653bc2
Merge pull request #1517 from broadinstitute/rhl_adapter_boundary_err_1406
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Fix adapter bounday for positive strand
2016-11-18 10:25:46 -05:00
22d94a7096
Fix adapter bounday for positive strand
2016-11-16 16:41:17 -05:00
6156b85ad9
Fixed logic error and tidied AlleleBalance and AlleleBalanceBySample
2016-11-16 14:10:48 -05:00
d61b4c7e91
Change the truth VCF
2016-11-15 14:56:15 -05:00
2b83dd7c5b
Added TreeReduce interface to VariantFiltration
2016-11-14 17:19:44 -05:00
bcbd7fe952
Change default value of STANDARD_CONFIDENCE_FOR_CALLING to 10
2016-11-11 02:06:41 -05:00
df0ba2ce8d
BaseCountsBySample counting bases at a particular position
2016-11-08 13:31:05 -05:00
029632eb1c
backport numerics changes in new qual
2016-11-01 03:16:21 -04:00
cc91052e69
fixed a max priority Q error while removing alt alleles when faced with high ploidy and allele count; added hackish integration test ( #1457 )
2016-10-27 11:19:49 -04:00
01a858542f
Remove RankSumTest and RMSAnnotation from hom-ref sites
2016-10-14 11:34:54 -04:00
16417bbf34
Fixes NaN issue in new Qual calculator
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Fixes issue #1491
2016-10-11 16:03:06 -04:00
81a9ece45b
deprecate -stand_emit_conf
2016-10-09 10:24:09 -04:00
4ef396f72e
Assign correct ambiguity code for * allele
2016-09-22 11:02:44 -04:00
318bee2269
Backport new AFCalculator
2016-09-21 15:21:56 -04:00
c13e3752d6
Move htsjdk to ver 2.6.1 and picard to ver 2.6.0
2016-09-16 16:36:52 -04:00
6564066de3
Remove NON_REF from allSites VCF output
2016-09-16 13:55:52 -04:00
091d05370b
Fix 1448 to make alt allele removal by likelihoods robust to ref allele indices ( #1475 )
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* alt alle removal by likelihoods now robust to ref allele indices (no longer assumes 0-indexed ref)
2016-09-13 21:20:44 -04:00
a7b1130224
Do not emit GVCF block definitions in the header
2016-09-09 07:41:03 -04:00
956b18fbb7
Make ReadPosRankSumTest.isUsableRead() account for deletions
2016-09-07 13:52:09 -04:00
3c88e6859f
fix 1430 for genotype filters; refactored filter() method; added unit and integration test; more comprehensive fix must be done first on htsjdk side in JEXLMap ( #1456 )
2016-09-06 17:30:18 -04:00
601c26a592
More small refactorings of Mutect2 code
2016-08-29 12:45:13 -04:00
a883905101
Remove -stand_emit_conf argument
2016-08-26 22:09:11 -04:00
bc3b3ac0ec
Cleaned up SomaticGenotypingEngine::callMutations and added some TODOs.
2016-08-26 14:12:05 -04:00
4aede99697
Merge pull request #1453 from broadinstitute/db_mutect2
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Lots of small improvements to Mutect2 code
2016-08-23 18:35:38 -04:00
cd5c04f806
Make getElementForRead() in RankSumTest robust
2016-08-23 14:56:32 -04:00
01142dfb1c
Lots of small improvements to Mutect2 code
2016-08-23 09:50:48 -04:00
abc4d5b7b3
Bypass spanning deletions in Rank Sum tests
2016-08-17 14:02:22 -04:00
3510906c7f
addresses issue #1280 now interval padding works for exclude intervals
2016-08-10 13:45:45 -04:00
49507faaa3
Changed maximum allowed GQB value to 100.
2016-08-05 13:06:31 -04:00
a465c87ff8
Added support for directly reading SRA runs
2016-08-02 15:21:14 -04:00
Ron Levine
Geraldine Van der Auwera
meganshand
David Benjamin
Steve Huang
Valentin Ruano Rubio
Takuto Sato
Peter Fan
Samuel Lee
Andrii Nikitiuk