a883905101
Remove -stand_emit_conf argument
2016-08-26 22:09:11 -04:00
cb0dedeb49
Merge pull request #1462 from broadinstitute/ts_m2_refactor
...
Clean up SomaticGenotypingEngine::callMutations and add TODOs
2016-08-26 14:15:33 -04:00
bc3b3ac0ec
Cleaned up SomaticGenotypingEngine::callMutations and added some TODOs.
2016-08-26 14:12:05 -04:00
4aede99697
Merge pull request #1453 from broadinstitute/db_mutect2
...
Lots of small improvements to Mutect2 code
2016-08-23 18:35:38 -04:00
53e1d42d28
Merge pull request #1460 from broadinstitute/rhl_rank_sum_test_del_return
...
Make getElementForRead() in RankSumTest robust
2016-08-23 16:36:30 -04:00
cd5c04f806
Make getElementForRead() in RankSumTest robust
2016-08-23 14:56:32 -04:00
01142dfb1c
Lots of small improvements to Mutect2 code
2016-08-23 09:50:48 -04:00
ebceb06284
Merge pull request #1445 from broadinstitute/rhl_read_pos_span_del
...
Ignore spanning deletions in Rank Sum tests
2016-08-17 20:21:47 -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
...
addresses issue #1280 now interval padding works for exclude intervals
2016-08-17 13:15:15 -04:00
27e56b2bb9
Merge pull request #1441 from broadinstitute/rhl_printreads_bqsr_fail
...
Throw an exception if the BQSR input covariants file is not found
2016-08-11 16:16:08 -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
7959324f08
Merge pull request #1451 from broadinstitute/sl_issue_1345_fix_2
...
Changed maximum allowed GQB value to 100.
2016-08-05 15:12:20 -04:00
49507faaa3
Changed maximum allowed GQB value to 100.
2016-08-05 13:06:31 -04:00
0630c7befd
Merge pull request #1423 from broadinstitute/rhl_read_sra
...
Added support for directly reading SRA runs
2016-08-02 18:10:33 -04:00
a465c87ff8
Added support for directly reading SRA runs
2016-08-02 15:21:14 -04:00
6bca5a060f
Merge pull request #1446 from broadinstitute/sl_issue_1345_fix
...
Fixed MD5 broken by PR #1440 .
2016-07-27 21:53:00 -04:00
832a383acd
Fixed MD5 broken by PR #1440 .
2016-07-27 13:51:20 -04:00
9a6ce7a347
Merge pull request #1440 from broadinstitute/sl_issue_1345
...
Added exception for GQB values greater than MAX_GENOTYPE_QUAL and tests.
2016-07-26 14:55:59 -04:00
e194b52ef3
Merge pull request #1442 from broadinstitute/vrr_genotype_gvcf_performance_fix
...
GenotypeGVCFs performance and QUAL miscalculation fix applied to master.
2016-07-26 13:13:52 -04:00
fef63ce6a8
Make sure that multi-alleleic uninformative PLs (0,0,...,0) stay uninformative after biallelization.
...
Addresses issue #1439 (thus #1437 ).
Fixes a bug where non informative PLs were not handled appropriatelly when calculating multi-allelic site QUAL values.
This was resulting in long execution times for very large datasets (~200,000 samples in the case of ExAC2).
2016-07-25 17:19:03 -04:00
3daed9e5a1
Added exception for GQB values greater than MAX_GENOTYPE_QUAL and tests.
2016-07-20 16:48:59 -04:00
b4eb479727
Merge pull request #1417 from broadinstitute/rhl_ggvcf_span_del
...
Removed spanning deletions if the deletion was removed
2016-07-19 16:55:06 -04:00
7392c4d1b0
Removed spanning deletions if the deletion was removed
2016-07-19 12:23:49 -04:00
b6908f52f0
Merge pull request #1432 from broadinstitute/rhl_invalid_intervals
...
Throw an exception for invalid Picard intervals
2016-07-15 13:02:39 -04:00
4f2e312805
Throw an exception for invalid Picard intervals
2016-07-15 11:20:53 -04:00
c406102e03
Merge pull request #1436 from broadinstitute/ldg_fixBetaTestingAnnotationGroup
...
Fixed the BetaTesting annotation group
2016-07-13 16:23:19 -04:00
641382eb8b
Fix BetaTestingAnnotation group
...
Add test
2016-07-13 16:05:21 -04:00
5255435f0e
Merge pull request #1433 from broadinstitute/rhl_progress_meter_periodicity
...
Enable control of reporting periodicity
2016-07-13 10:14:01 -04:00
aace73e884
Enable control of reporting periodicity
2016-07-13 07:24:03 -04:00
5e39b59ef3
Merge pull request #1429 from broadinstitute/ts_readpos_filter
...
Port MuTect1 Clustered Read Position filter to MuTect2
2016-07-12 08:30:51 -04:00
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
...
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
...
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
...
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.
...
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
...
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
...
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
...
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
...
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
...
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
...
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
...
Improve documentation of read filter
2016-06-23 22:11:25 -04:00
Ron Levine
Takuto Sato
David Benjamin
Peter Fan
Peter Fan
samuelklee
Samuel Lee
Andrii Nikitiuk
Valentin Ruano Rubio
ldgauthier
Steve Huang
meganshand
Geraldine Van der Auwera