741c544fbf
Deprecate --allowMissingData, add --errorIfMissingData and print NA for null object in VariantsToTable
2017-06-28 12:54:07 -04:00
0f8818bc43
Update all the md5s for header reference path changes
2017-06-26 15:53:13 -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
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
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
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
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
a8f70c891f
Create GMM from model reports in VQSR
2017-04-26 16:02:06 -04:00
4fe4ace232
minor bug fix in depth of coverage for partitioning by library + test ( #1574 )
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minor bug fix in depth of coverage for partitioning by library
2017-04-26 10:42:54 -04:00
a950d0778f
Add the Intel GKL as a dependency, and turn on the Intel inflater/deflater by default
2017-04-05 12:45:26 -04:00
278985b8bd
Update PLINK link and change lines to columns
2017-03-23 11:46:38 -04:00
4188745074
Document how VTT orders samples in output table
2017-03-21 18:04:38 -04:00
687dee22ac
Fix CombineVariants merge for different types
2017-03-14 16:42:16 -04:00
1e88d849e3
Fixed ClippingOP.getNewAlignmentStartOffset() to handle N cases properly and added unit test
2017-03-06 15:40:01 -05:00
91339c12c9
Move htsjdk to ver 2.9.1 and picard to ver 2.9.0
2017-02-22 19:01:26 -05:00
61875e4dfa
Fix LeftAlignAndTrimVariants -split to not change no-call genotypes to hom-ref
2017-02-22 17:57:59 -05:00
ab75b08ea7
Remove unused compressed_block_size and close BlockCompressedInputStream
2017-02-17 12:22:53 -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
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
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
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
262c08aee3
Make exit system file type message generic
2016-11-23 10:12:21 -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
2d06f33227
Set HTSJDK log level
2016-11-15 07:08:19 -05:00
2b83dd7c5b
Added TreeReduce interface to VariantFiltration
2016-11-14 17:19:44 -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
d7090ef158
Write saved WARN messages to stderr instead of stdout
2016-10-21 13:01:07 -04:00
0d2a3e754c
Merge pull request #1490 from broadinstitute/rhl_ggvcf_hom_ref_high_mq
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Remove RankSumTest and RMSAnnotation from hom-ref sites
2016-10-14 14:41:49 -04:00
01a858542f
Remove RankSumTest and RMSAnnotation from hom-ref sites
2016-10-14 11:34:54 -04:00
cfd3ffa2c0
Replace SAMFileReader with calls to SamReaderFactory
2016-10-14 11:22:54 -04:00
a301ba1977
Add read group identifier to column names
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If two SAMReadGroupRecords share the same sample name, the output will contain duplicate column headers.
This PR fix the problem.
2016-10-11 18:37:11 -04:00
2c83081560
Remove sra group
2016-09-23 17:39:10 -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
ab454e8812
Upgrade Apache Commons Collections to version 3.2.2
2016-09-07 18:59:21 -04:00
Ron Levine
Laura Gauthier
droazen
Ernesto Brau
Samuel Friedman
Samuel Friedman
skwalker
Geraldine Van der Auwera
David Benjamin
Pierre Lindenbaum