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
c4a06ad20a
Move indel realignment to public
2016-05-27 12:39:58 -04:00
3b7e0c56bf
Moved post-IR MQ reverter filter to public
2016-05-27 12:39:58 -04:00
e74a41e158
Merge pull request #1377 from broadinstitute/vrr_non_ref_likelihood_recal
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Fix for the sum(AD) > DP bug.
2016-05-26 22:35:53 -04:00
9d32dec9cd
Fix for the sum(AD) > DP bug.
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Closes issue #1340
2016-05-26 15:04:52 -04:00
25fa25b618
Added option to validate gvcf (for ValidateVariants) ( #1379 )
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* with option --gvcf CLP will now put extra checks that a gvcf must adhere to (existance of <NON_REF> allele at every variant, and that the variants in total cover the entire requested intervals, or the whole genome if no intervals have been specified)
* works on gvcf produced by HC when using either GVCF or BP_RESOLUTION mode
* added positive and negative tests
2016-05-26 06:42:45 -04:00
e1fadae139
Fix error in InfiniteRandomMatingPopulationModel.getLikelihoodsCalculator
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Same issue noticed in GATK4 [here](https://github.com/broadinstitute/gatk/issues/1856 )
2016-05-25 17:23:26 -04:00
2c8356519c
Merge pull request #1375 from broadinstitute/gvda_fix_offbyone_maxAltAlls_M2_#1297
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Fixed M2 max alt alleles threshold evaluation error
2016-05-19 13:59:02 -04:00
7fdd3c2a0c
Merge pull request #1358 from broadinstitute/sl_issue_1327
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Changed calls with GQ=0 to no-call for HaplotypeCaller in normal mode.
2016-05-19 12:26:35 -04:00
edd9fcb7e5
Merge pull request #1370 from broadinstitute/ldg_fixBQresMQ
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Add fix and test for finalizing MQ annotation at BP resolution for va…
2016-05-19 09:39:07 -04:00
644076b1e1
Add fix and test for finalizing MQ annotation at BP resolution for variant and ref samples
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Addresses issue #1356
2016-05-19 08:15:30 -04:00
f5456a3761
Fixed M2 max alt alleles threshold evaluation error
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Also clarified some argument docs
2016-05-18 21:54:30 -04:00
ff532ed0cd
Merge pull request #1352 from broadinstitute/mf_othersrequired
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Adds othersRequired so that some arguments can require other arguments in order to work.
2016-05-18 15:14:59 -04:00
bf4b1a5421
Changed calls for GQ=0 from 0/0 to ./. for HaplotypeCaller in normal mode.
2016-05-18 13:17:27 -04:00
Valentin Ruano Rubio
Ron Levine
Geraldine Van der Auwera
sooheelee
samuelklee
Samuel Lee
Yossi Farjoun
Steve Huang
ldgauthier
Mark Fleharty