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
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
abc4d5b7b3
Bypass spanning deletions in Rank Sum tests
2016-08-17 14:02:22 -04:00
01fdb90096
Merge pull request #1452 from broadinstitute/pf_excludeIntervalPadding
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addresses issue #1280 now interval padding works for exclude intervals
2016-08-17 13:15:15 -04:00
f6c18a5182
Throw an exception if the BQSR input covariants file is not found
2016-08-11 12:46:14 -04:00
3510906c7f
addresses issue #1280 now interval padding works for exclude intervals
2016-08-10 13:45:45 -04:00
a465c87ff8
Added support for directly reading SRA runs
2016-08-02 15:21:14 -04:00
4f2e312805
Throw an exception for invalid Picard intervals
2016-07-15 11:20:53 -04:00
641382eb8b
Fix BetaTestingAnnotation group
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Add test
2016-07-13 16:05:21 -04:00
aace73e884
Enable control of reporting periodicity
2016-07-13 07:24:03 -04:00
d6d0678b50
Build on Laura's code and finish porting MuTect1 clustered read position filter.
2016-07-11 17:33:08 -04:00
9b32cf5291
Fixed merging of GVCF blocks by fixing rounding of GQ values in ReferenceConfidenceModel.
2016-07-06 10:08:08 -04:00
2c94f74a95
Merge pull request #1404 from broadinstitute/ldg_M2_addM1filters
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MuTect 2: port strand artifact filter from MuTect 1
2016-07-05 13:27:35 -04:00
1ff234e7dd
remove alt alleles, when genotype count is explosively large, based on alleles' highest supporting haplotype score; max tolerable genotype count is controlled by a default value overridable by user
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remove alt alleles, when genotype count is explosively large, based on alleles' highest supporting haplotype score; max tolerable genotype count is controlled by a default value overridable by user
2016-06-30 22:36:49 -04:00
63e0865491
Built on Laura's code to port the strand bias filter from M1 and refactored code aroud SomaticGenotypingEngine. Added a new integration test.
2016-06-29 22:46:40 -04:00
556cc69185
Fix for int overflow in RankSum calculation
2016-06-29 12:02:13 -04:00
07052ba8ea
Changes to use the median rather than the second best likelihood for the NON_REF allele
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Addresses issue #1378 following the first proposal using the 'median' rather than the 'mean'.
2016-06-28 13:10:22 -04:00
3c5eac8c17
Move htsjdk and picard to version 2.5.0
2016-06-28 09:42:32 -04:00
6fe80d53d0
Improve documentation
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Clarified that this also filters supplementary alignments.
2016-06-23 16:20:00 -04:00
c6ef81b611
Change HashMap to LinkedHashMap for predictable ordering
2016-06-23 10:48:22 -04:00
76bb8fd9e5
Allows GatherBqsrReports to accept a .list file as input.
2016-06-22 12:39:18 -04:00
427645162b
SelectVariants works with non-diploids
2016-06-21 12:26:13 -04:00
f0f482c1fe
- added an option to merge GenomeLocs that are abutting (contiguous) rather than actually overlapping. ( #1399 )
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- this should make ValidateVariants much faster.
- fixed NPE that occurs when there is no -L argument
2016-06-06 11:46:15 -04:00
Ron Levine
Geraldine Van der Auwera
David Benjamin
Pierre Lindenbaum
Steve Huang
Peter Fan
Peter Fan
Andrii Nikitiuk
Laura Gauthier
Takuto Sato
Samuel Lee
meganshand
Valentin Ruano Rubio
sooheelee
Yossi Farjoun