zzh
266936ed73
添加ProtectedCLGATK类，方便调试protect模块中的代码
2026-01-07 18:21:50 +08:00
zzh
56e0098a71
忽略target子文件夹
2026-01-05 19:02:51 +08:00
aa8764d6c3
Update pom versions for the 3.8-1 release
2017-11-09 02:10:43 -05:00
e4c24188b2
Merge remote-tracking branch 'unstable/master'
2017-11-09 02:09:51 -05:00
c654e0b9a2
Update pom versions to mark the start of GATK 3.9 development
2017-11-09 02:09:16 -05:00
a2f45944f3
Serialized GMM no longer depends on command line annotation order ( #1632 )
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Order annotations by the order in the model report.
2017-10-24 11:50:03 -04:00
09b4cf70f6
Upgrade GKL to 0.6.0 ( #1631 )
2017-09-29 22:15:43 -04:00
76c9902fbf
Update GKL to 0.5.9 ( #1629 )
2017-09-06 17:25:23 -04:00
a9479ee43e
Revert "Changed GKL version to 0.5.6 ( #1626 )" ( #1628 )
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This reverts commit 78acfb95f8672a7fd65c66e0932a0d3b212ec8d8.
2017-08-29 11:05:04 -04:00
effaf881b3
Changed GKL version to 0.5.6 ( #1626 )
2017-08-29 10:48:26 -04:00
aa8b2ab535
Change to GKL 0.5.5, which fixes a bug in FPGA 'private' mode ( #1623 )
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Update GKL to version 0.5.5, which fixes a bug in FPGA 'private' mode. Integration test results were updated to reflect different fallback behavior when AVX is not available.
2017-08-18 22:51:33 -04:00
3c841eaab5
Merge pull request #1622 from broadinstitute/rhl_vtt_fix_doc_typos
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Fix VariantsToTable documentation typos
2017-08-07 17:45:06 -04:00
9ba104a6e9
Merge pull request #1625 from broadinstitute/ldg_fixPLsubsettingGQproblem
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Update the GQ after PLs get subset
2017-08-07 17:43:49 -04:00
d28b086862
Update the GQ after PLs get subset
2017-08-04 09:54:08 -04:00
afc257c195
Fix VariantsToTable documentation typos
2017-07-29 08:33:14 -04:00
02c8302290
Update pom versions to mark the start of GATK 3.9 development
2017-07-28 10:14:19 -04:00
5381dc83b1
Update pom versions for the 3.8 release
2017-07-28 10:01:54 -04:00
57929e2a7b
Merge remote-tracking branch 'unstable/master'
2017-07-28 10:00:40 -04:00
1798afb1f4
Merge pull request #1621 from broadinstitute/gvda_clean_slate
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Clean slate for the 3.8 release
2017-07-28 00:35:00 -04:00
04a688f701
Update release scripts
2017-07-28 00:32:05 -04:00
8af62576cf
Updated gatkdocs template
2017-07-28 00:30:56 -04:00
be523df1b1
Fix problem filename
2017-07-27 22:40:42 -04:00
a906e24010
Merge pull request #1615 from broadinstitute/gvda_archive_docs
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Archive GATK3-specific docs from the forum
2017-07-24 02:46:05 +02:00
3f3ef608e5
Archive GATK3-specific docs from the forum
2017-07-24 00:57:50 +02:00
6de68d556e
Merge pull request #1609 from broadinstitute/yf_make_readutils_test_public
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making a test within readutils-test public
2017-07-23 23:18:10 +02:00
57588a5661
Make error informative for non-diploid family likelihoods
2017-07-21 11:07:02 -04:00
e406bb76ea
Move htsjdk to ver 2.10.1 and picard to ver 2.10.2
2017-07-18 13:16:21 -04:00
97ed131abd
Merge pull request #1610 from broadinstitute/ldg_fixRankSumHistogramOutput2
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Changed ASRankSum single-sample output so it's combine-able
2017-07-18 12:51:24 -04:00
66f5fe075b
Changed ASRankSum single-sample output so it's combine-able
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single sample gVCF now gets a "histogram" with one entry
2017-07-18 11:00:59 -04:00
385f06b5cb
Merge pull request #1608 from broadinstitute/ldg_renomalizeVQSRdata
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Normalize input data by same annotation normalization scheme as input…
2017-06-30 16:44:40 -04:00
ee39f9141f
Normalize input data by same annotation normalization scheme as input model
2017-06-30 11:52:12 -04:00
d535c377b5
- responding to reviewer's comments.
2017-06-28 16:40:55 -04:00
741c544fbf
Deprecate --allowMissingData, add --errorIfMissingData and print NA for null object in VariantsToTable
2017-06-28 12:54:07 -04:00
14e598a401
Merge pull request #1605 from broadinstitute/ldg_updateReference
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Update all the md5s for header reference path changes
2017-06-27 08:29:09 -04:00
0f8818bc43
Update all the md5s for header reference path changes
2017-06-26 15:53:13 -04:00
71e361dae9
Merge pull request #1604 from broadinstitute/rhl_close_printstream_1600
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Close BQSRGatherer's PrintStream when finished
2017-06-26 13:58:52 -04:00
312d97d53b
Close BQSRGatherer's PrintStream when finished
2017-06-26 13:47:30 -04:00
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
ba7df054f0
Close BQSRGatherer's PrintStream when finished
2017-06-24 15:09:41 -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
c855714e10
Merge pull request #1586 from broadinstitute/ldg_turnOffOneMoreTest
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One more stupid fargo bam test to turn off
2017-05-11 12:17:11 -04:00
417d390077
One more stupid fargo bam test to turn off
2017-05-11 09:54:38 -04:00
ae174d3359
Merge pull request #1541 from broadinstitute/ldg_revertToMedianRankSum
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Changed calculation of allele-specific rank sum so it's now the median of the per-sam…
2017-05-10 14:43:08 -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
zzh
Geraldine Van der Auwera
Samuel Friedman
Ernesto Brau
Laura Gauthier
Ron Levine
Yossi Farjoun
droazen
Ernesto Brau