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molgenis
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vip
Variant Interpretation Pipeline
https://molgenis.github.io/vip/
GNU Lesser General Public License v3.0
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VIP errors if 2 filenames in the input are identical
#491
bartcharbon
opened
1 year ago
0
filter samples somehow removes some INFO headers
#490
bartcharbon
opened
1 year ago
0
Error merging SVs: The REF prefixes differ: A vs N (1,1)
#489
bartcharbon
opened
1 year ago
1
Test runner: caching, parallelization, test selection
#488
dennishendriksen
closed
1 year ago
0
Run GADO only once per project
#487
bartcharbon
closed
1 year ago
0
Swap SV and Gnomad filter blocks in the tree
#486
bartcharbon
closed
1 year ago
0
Fix install.sh: download unzipped ref index files
#485
dennishendriksen
closed
1 year ago
0
Fix ClinVar annotations with null values
#484
dennishendriksen
closed
1 year ago
0
fix: revert removal of unzip_reference
#483
dennishendriksen
closed
1 year ago
0
Validate that input contigs exist in reference
#482
dennishendriksen
closed
1 year ago
0
Configure GLnexus preset per sequencing method
#481
dennishendriksen
closed
1 year ago
0
Do not publish intermediate deep variant chunked vcfs
#480
dennishendriksen
closed
1 year ago
0
Improve test runtime for illumina data in combination with deepvariant
#479
bartcharbon
closed
1 year ago
1
Change .g.vcf merge preset default to 'DeepVariant'
#478
dennishendriksen
closed
1 year ago
0
Fix possible deepvariant tmp dir error
#477
dennishendriksen
closed
1 year ago
0
Improve test runtime for illumina data in combination with deepvariant
#476
bartcharbon
closed
1 year ago
0
Fix possible deepvariant tmp dir error
#475
dennishendriksen
closed
1 year ago
0
Log test error messages to console
#474
bartcharbon
closed
1 year ago
0
GIAB tests
#473
dennishendriksen
closed
1 year ago
0
Fix #471 cram_str_straglr_call can produce unsorted vcf
#472
dennishendriksen
closed
1 year ago
0
`nf-cram_str_straglr_call` can produce unsorted `vcf`
#471
dennishendriksen
closed
1 year ago
0
additional sample validation rules
#470
dennishendriksen
closed
1 year ago
0
Add AlphScore to default decision tree
#469
bartcharbon
closed
1 year ago
0
fix #467 Report with long-read alignment hangs
#468
dennishendriksen
closed
1 year ago
0
Add AlphScore to default decision tree
#466
bartcharbon
closed
1 year ago
0
Fix: gvcf workflow results might be invalid for multi-sample projects
#465
dennishendriksen
closed
1 year ago
0
Fix create_inheritance.sh: update incomplete penetrance file path
#464
bartcharbon
closed
1 year ago
0
Fix #244 gnomAD and ClinVar annotations can be incorrect
#463
dennishendriksen
closed
1 year ago
0
chore:bump dependencies
#462
dennishendriksen
closed
1 year ago
0
chore:bump version v5.8.2 to v6.0.0
#461
dennishendriksen
closed
1 year ago
0
Reintroduce deep variant
#460
bartcharbon
closed
1 year ago
0
Improve AlphScore VEP plugin performance, fix VKGL GRCh38 resource
#459
dennishendriksen
closed
1 year ago
0
Fix GADO warning, small improvements
#458
dennishendriksen
closed
1 year ago
0
Fix gitignore for vep plugins
#457
bartcharbon
closed
1 year ago
0
Fix filename for AlphScore resource
#456
bartcharbon
closed
1 year ago
0
Feat/alph score
#455
bartcharbon
closed
1 year ago
0
Report crashed in detail view for long read data (reads to big for genome browser)
#467
bartcharbon
closed
1 year ago
1
Fix VEP plugins returning () instead of {}
#454
bartcharbon
closed
1 year ago
0
Add AlphScores to VIP
#453
bartcharbon
closed
1 year ago
0
Update test_gvcf.sh: enable test
#452
dennishendriksen
closed
1 year ago
0
fix GLnexus memory usage: stick to limits and parallelize
#451
dennishendriksen
closed
1 year ago
0
fix GADO VEP plugin: NPE in print statement
#450
dennishendriksen
closed
1 year ago
0
bump vkgl_consensus_20230401 to vkgl_consensus_20230701
#449
dennishendriksen
closed
1 year ago
0
fix github pages deploy: replace action with Travis
#448
dennishendriksen
closed
1 year ago
0
fix:install correct hpo resource
#447
dennishendriksen
closed
1 year ago
0
bump vcf-inheritance-matcher 2.1.6 to 2.1.7
#446
dennishendriksen
closed
1 year ago
0
Add default error strategy with backoff
#445
bartcharbon
closed
1 year ago
0
New HPO + GADO 1.0.3
#444
bartcharbon
closed
1 year ago
0
Add Stranger for str annotation
#443
bartcharbon
closed
1 year ago
0
Small fixes (stubbing params, cram param in VCF workflow)
#442
bartcharbon
closed
1 year ago
0
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