d6d0678b50
Build on Laura's code and finish porting MuTect1 clustered read position filter.
2016-07-11 17:33:08 -04:00
77d8da6bb2
Merge pull request #1431 from broadinstitute/sl_issue_1345
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Fixed merging of GVCF blocks by fixing rounding of GQ values in ReferenceConfidenceModel.
2016-07-06 11:46:39 -07:00
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
9c3b928945
Merge pull request #1428 from broadinstitute/vrr_issue_1419_out_of_mem_genotype_gvcfs
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RCM Variant sites merger won't output PL when there are too many alle…
2016-07-01 13:58:38 -04:00
45607d1b30
RCM Variant sites merger won't output PL when there are too many alleles in order to avoid memory issues with large cohort runs.
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Small additional "cosmetic" changes to the code
Addresses issue #1419 .
2016-07-01 11:33:07 -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
6471bda0cd
Merge pull request #1426 from broadinstitute/ms_excessHetSmallP
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Changes max value output for ExcessHet
2016-06-30 08:26:01 -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
4066bcd75c
Add new annotator for M1 clustered read position filter and M1 strand bias filter.
2016-06-29 22:46:37 -04:00
1b921666a7
Change to max value of ExcessHet
2016-06-29 16:33:50 -04:00
db196e709a
Merge pull request #1424 from broadinstitute/ms_rankSumBug
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Fixes Overflow in Rank Sum With Large Pileups
2016-06-29 13:26:28 -04:00
556cc69185
Fix for int overflow in RankSum calculation
2016-06-29 12:02:13 -04:00
b14312a14d
Merge pull request #1389 from broadinstitute/vrr_non_ref_likelihoods_to_median
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Changes to use the median rather than the second best likelihood for …
2016-06-28 16:07:09 -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
b80a293848
Merge pull request #1422 from broadinstitute/rhl_htsjdk_picard_2.5.0
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Move htsjdk and picard to version 2.5.0
2016-06-28 12:16:04 -04:00
3c5eac8c17
Move htsjdk and picard to version 2.5.0
2016-06-28 09:42:32 -04:00
23c48bcdb1
Merge pull request #1415 from broadinstitute/shlee-addsupplementarytodocument
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Improve documentation of read filter
2016-06-23 22:11:25 -04:00
6fe80d53d0
Improve documentation
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Clarified that this also filters supplementary alignments.
2016-06-23 16:20:00 -04:00
4eff18a470
Merge pull request #1414 from broadinstitute/rhl_sv_hashmap
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Change HashMap to LinkedHashMap for predictable iteration order.
2016-06-23 12:22:43 -04:00
c6ef81b611
Change HashMap to LinkedHashMap for predictable ordering
2016-06-23 10:48:22 -04:00
679941c1b1
Merge pull request #1412 from broadinstitute/sl_issue_1285
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Allows GatherBqsrReports to accept a .list file as input.
2016-06-22 15:25:19 -04:00
76bb8fd9e5
Allows GatherBqsrReports to accept a .list file as input.
2016-06-22 12:39:18 -04:00
ae8ab33cdd
Merge pull request #1408 from broadinstitute/rhl_sv_non_diploids
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SelectVariants works with non-diploids
2016-06-21 13:52:07 -04:00
427645162b
SelectVariants works with non-diploids
2016-06-21 12:26:13 -04:00
d3862459e9
Merge pull request #1410 from broadinstitute/vrr_bug_1407_no_such_element_exception
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Fixes bug #1407
2016-06-20 15:52:25 -04:00
857459e420
Silly mistake '<' for a '<='. It was causing the exception when the exact number of alleles to drop was matching MAX_DROPPED_ALTERNATIVE_ALLELES_TO_LOG exactly (fixed to 20).
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I change the code to impose a maximum allele list message length instead and in the process I fixed the bug.
2016-06-17 15:22:59 -04:00
6b04f6ae14
Merge pull request #1405 from broadinstitute/sl_issue_1281
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Added regression test for genotyping of spanning deletions in GenotypeGVCFs.
2016-06-15 13:59:14 -04:00
e119feee61
Added regression test for genotyping of spanning deletions in GenotypeGCVFs.
2016-06-15 09:48:26 -04:00
050bcbb06b
Merge pull request #1403 from broadinstitute/rhl_ggvcf_max_num_pls
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Add integration test using -maxNumPLValues for GenotypeGVCFs
2016-06-08 12:54:19 -04:00
ba2e7be05b
Add integration test using -maxNumPLValues for GenotypeGVCFs
2016-06-07 14:38:12 -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
85dce75f3f
Update pom versions to mark the start of GATK 3.7 development
2016-06-01 17:21:48 -04:00
f185a75e1c
Update pom versions for the 3.6 release
2016-06-01 17:08:17 -04:00
6ba2e38a5c
Merge remote-tracking branch 'unstable/master'
2016-06-01 17:04:21 -04:00
b95b76b0e2
Merge pull request #1394 from broadinstitute/gvda_add_colt_dependency
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Add colt > cern.jet.normal dependency
2016-06-01 14:16:57 -04:00
bd2626bea2
Add colt > cern.jet.normal dependency
2016-06-01 13:24:50 -04:00
8b24e3bd65
Merge pull request #1391 from broadinstitute/rhl_htsjdk_picard_2.4.1
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Move htsjdk and picard to version 2.4.1
2016-06-01 06:49:16 -04:00
30665c7dbc
Move Move htsjdk and picard to version 2.4.1
2016-05-31 22:36:38 -04:00
801aa49d25
Merge pull request #1392 from broadinstitute/gvda_vqsr_retries_mdp
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Ability to retry building VQSR model (contributed by mdp)
2016-05-31 21:35:27 -04:00
a76cb052e2
Ability to retry building VQSR model (contributed by mdp)
2016-05-31 18:57:55 -04:00
e2634e56a9
Merge pull request #1387 from broadinstitute/gvda_gatkdocs_enhancements
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GATKDocs overhaul
2016-05-31 17:15:18 -04:00
d87345cd1d
GATKDocs overhaul
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- Fixed displaying of default values
- Removed code cruft
- Reorganized tooldoc categories and improved names
- Reorganized tools within categories where applicable
- Touched up various tool docs
- Switched default gatkdocs output to html
- Added parameter in agrregator pom to control output type
- Set gatkdocs publishing script to output php
- Deprecated GenotypeAndValidate walker
- Added back PhoneHome arguments with @Deprecated annotations
2016-05-29 16:35:08 -04:00
f77735cdde
Merge pull request #1388 from broadinstitute/gvda_disable_phone_home
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Remove Phone Home
2016-05-27 19:55:57 -04:00
0769c8ae3e
Remove Phone Home
2016-05-27 16:16:29 -04:00
15f3f902f7
Merge pull request #1374 from broadinstitute/gvda_move_ReassignOriginalMQAfterIndelRealignment_toPublic_#1364
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Code cleanup campaign pre-3.6; see itemized commit messages.
2016-05-27 16:07:14 -04:00
efbbbb1bd9
Add M2 to the HC annotations check
2016-05-27 13:49:31 -04:00
5b80c92cb7
Improved article linking in error messages
2016-05-27 13:49:31 -04:00
3cc7d7e56d
Hide deletion arguments in ASEReadCounter
2016-05-27 12:46:13 -04:00
81d4eaea29
Fixed warnings in LAATV and ValidateVariants
2016-05-27 12:46:02 -04:00
Takuto Sato
samuelklee
Samuel Lee
Valentin Ruano Rubio
Steve Huang
meganshand
Laura Gauthier
Ron Levine
Geraldine Van der Auwera
sooheelee
Yossi Farjoun