fff63bab53
Merge pull request #1595 from broadinstitute/eba_gkl_pairhmm_fpga
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Added FPGA support for PairHMM via GKL, and marked as 'experimental'
2017-06-26 12:06:31 -04:00
18c9fe41c7
Close SamReader
2017-06-08 14:45:29 -04:00
446b11913b
Added FPGA support for PairHMM via GKL, and marked as 'experimental'
2017-06-07 14:39:11 -04:00
e8b42c4dfd
Use GKL's implementation of Vector Logless Pair HMM
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Fixed MuTect2 tests by removing old -alwaysloadVectorHmm flag; upgraded to GKL 0.5.2; FASTEST_AVAILABLE pairhmm option; improved documenting comments in code
Made FASTEST_AVAIALABLE the default for the pairHMM cmdline argument
Make LOGLESS_CACHING the default pairHMM unified cmdline argument, fix error message if choose an unrecognized pairHMM
Updae MD5s
2017-06-07 13:33:32 -04:00
70b2575c29
Move htsjdk to ver 2.10.0 and picard to ver 2.9.2
2017-06-02 06:52:24 -04:00
3de98263f5
Copy Program Records (PG) from input BAM
2017-06-01 16:01:20 -04:00
1d6756fbd0
Add assert to testMissingAlleleSpecificAnnotationGroup ( #1587 )
2017-05-12 17:07:05 -04:00
4a0458b2e9
GenotypeGVCFs and CombineGVCFs should error when AS annotations are not present ( #1585 )
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GenotypeGVCFs and CombineGVCFs error when missing the allele specific annotation group
2017-05-11 12:41:51 -04:00
35d0b72c79
Changed calculation of rank sum so it's now the median of the per-sample rank sums (because the rank sum across all sample data did worse for biallelics). Now only called alt for 0/1s has rank sum, similar to old paradigm. Combined gVCF rank sums stored in Histogram, then median is taken once during genotyping. Histogram uses Integer keys to eliminate numerical precision mess
2017-05-10 09:04:42 -04:00
8703642142
Change AC>1 to AC>0
2017-05-09 13:31:58 -04:00
00b7135afe
Merge pull request #1575 from broadinstitute/snf_ReadGMMReport
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Read model report and reconstruct GMM from it in VQSR
2017-05-08 14:40:27 -04:00
ed440f1684
respond to review comments
2017-05-05 16:29:01 -04:00
68bdb93c8c
add annotation mismatch warning and refactor tests
2017-05-04 16:48:24 -04:00
f5d133df87
scientific notation in model report and basic test
2017-05-03 18:37:52 -04:00
4df71a3ca1
expect floats in the report
2017-05-02 12:05:10 -04:00
505383e504
Remove obsolete unmapped reads test for FindCoveredIntervals ( #1580 )
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Remove obsolete unmapped reads test for FindCoveredIntervals
2017-05-02 08:50:12 -04:00
1b4ac51048
move model file parsing to initialize
2017-05-01 15:52:45 -04:00
d06a6c7318
string cast bug
2017-04-28 17:32:36 -04:00
ea5efa0b2c
Fixes rounding errors in FS using the same solution as R
2017-04-27 17:37:33 -04:00
f55b932cfc
addressed review comments
2017-04-27 17:16:57 -04:00
85cb1c2810
dont spam on NaNs
2017-04-26 17:33:06 -04:00
57c064eaa3
small code cleanup
2017-04-26 16:02:06 -04:00
a8f70c891f
Create GMM from model reports in VQSR
2017-04-26 16:02:06 -04:00
c20e682a97
Update MuTect2 documentation about not computing obvious germline variants
2017-03-21 17:54:52 -04:00
687dee22ac
Fix CombineVariants merge for different types
2017-03-14 16:42:16 -04:00
49083fc704
Fix FindCoveredIntervals so -minBQ, -minMQ and -cov work as expected
2017-03-07 16:58:23 -05:00
8316fa92f3
Set AD and DP to zero if no read coverage
2017-02-28 16:56:45 -05:00
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
droazen
Ron Levine
Ernesto Brau
Laura Gauthier
Sheila Chandran
Samuel Friedman
Samuel Friedman
meganshand
Geraldine Van der Auwera
David Benjamin