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
d512f3f808
Merge pull request #1582 from broadinstitute/SC-input-prior-HC-doc-fix
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Change AC>1 to AC>0
2017-05-09 14:15:42 -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
e9efd53281
Merge pull request #1581 from broadinstitute/ldg_actuallyFixTests
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Turn off one more test that needs the fargo bam
2017-05-03 09:59:20 -04:00
c91cacb642
Turn off one more unit test with fargo bam
2017-05-03 09:53:08 -04:00
67cf29558f
Merge pull request #1578 from broadinstitute/ldg_turnOffPicardAggregationTests
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Turn off PicardAggregation tests because they're a pain with all the …
2017-05-02 16:20:35 -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
2284a69e7c
Turn off PicardAggregation tests because they're a pain with all the bams moving to slow storage and because the pipeline utils aren't used anyway
2017-04-29 09:20:57 -04:00
d06a6c7318
string cast bug
2017-04-28 17:32:36 -04:00
31eee1f2a3
Merge pull request #1576 from broadinstitute/ms_FS_bug
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Fixes rounding errors in FS using the same solution as R
2017-04-28 17:02:09 -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
Geraldine Van der Auwera
Ron Levine
ldgauthier
Yossi Farjoun
droazen
Ernesto Brau
Sheila Chandran
Samuel Friedman
Samuel Friedman
meganshand