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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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Add Stragler for long read STR calling
#441
bartcharbon
closed
1 year ago
0
gVCF workflow
#440
dennishendriksen
closed
1 year ago
0
cuteSV can fail based on `~` content on host machine
#439
dennishendriksen
closed
1 year ago
0
Support .sam input in addition to .bam and .cram
#438
dennishendriksen
closed
1 year ago
0
Report can contain data of samples not in sample sheet
#437
dennishendriksen
closed
1 year ago
0
VCF index not created with HTSlib doesn't work
#436
dennishendriksen
closed
1 year ago
0
Succesfull pipeline execution if `individual_id` doesn't exist in vcf
#435
dennishendriksen
closed
1 year ago
0
Fix #432 annotate can fail with 'Failed to instantiate plugin GADO'
#434
dennishendriksen
closed
1 year ago
0
Fix #431 'Chromosome blocks not continuous' error
#433
dennishendriksen
closed
1 year ago
0
`annotate` can fail with 'Failed to instantiate plugin GADO'
#432
dennishendriksen
closed
1 year ago
1
`clair3_call` can fail with 'Chromosome blocks not continuous' error
#431
dennishendriksen
closed
1 year ago
0
`clair3 call` can fail due to cram-to-bam slice-and-convert issue
#430
dennishendriksen
closed
1 year ago
0
Feat/single thread bam convert
#429
bartcharbon
closed
1 year ago
1
Project samples must have same assembly and sequencing_method
#428
dennishendriksen
closed
1 year ago
0
Update nxf.config: fix VIP_VERSION
#427
dennishendriksen
closed
1 year ago
0
Add stranger def
#426
bartcharbon
closed
1 year ago
0
Add Straglr - long read short tandem repeat
#425
bartcharbon
closed
1 year ago
0
Bump vcf-report to 5.5.2
#424
bartcharbon
closed
1 year ago
0
SV calling cannot detect translocations due to chunking
#423
dennishendriksen
closed
1 year ago
0
bump vcf-report to 5.5.1, fix project_id param documentation
#422
dennishendriksen
closed
1 year ago
0
Add GADO docs
#421
bartcharbon
closed
1 year ago
0
feat: GnomAD HN Capice model
#420
SietsmaRJ
closed
1 year ago
0
Multi-project slice called too many times
#419
dennishendriksen
closed
1 year ago
0
Multi-project getProbands, getHpoIds, createPedigree incorrect
#418
dennishendriksen
closed
1 year ago
0
Chromosome blocks not continuous error in cram workflow
#417
bartcharbon
closed
1 year ago
1
M10277 Subworkflows & stubs (fix #405, fix #418, fix #419, fix #423, fix #428, fix #430, fix #435, fix #436, fix #437, fix #438, fix #439)
#416
dennishendriksen
closed
1 year ago
0
bump version
#415
bartcharbon
closed
1 year ago
0
Fix disable/enable cram feature
#414
bartcharbon
closed
1 year ago
0
bump vcf-report-5.4.0 to vcf-report-5.4.1
#413
dennishendriksen
closed
1 year ago
0
Feature: add GADO predictions
#412
bartcharbon
closed
1 year ago
0
Use nextflow environment variables if already exist
#411
bartcharbon
closed
1 year ago
0
docs:describe relationship to other licences
#410
dennishendriksen
closed
1 year ago
0
Add option to enable/disable crams in report
#409
bartcharbon
closed
1 year ago
0
Revert "gnomAD before annotSV"
#408
bartcharbon
closed
1 year ago
0
Docs fixes
#407
bartcharbon
closed
1 year ago
0
Workaround for N in REF of cuteSV
#406
bartcharbon
closed
1 year ago
0
Error if .cram doesn't contain reads for a chunk
#405
dennishendriksen
closed
1 year ago
0
Documentations improvements (annotations section, reference fasta warning)
#404
bartcharbon
closed
1 year ago
0
Revert "Test doc deployment"
#403
bartcharbon
closed
1 year ago
0
Test doc deployment
#402
bartcharbon
closed
1 year ago
0
Workaround for R in REF in cuteSV
#401
bartcharbon
closed
1 year ago
1
Bump vip version 5.6.0
#400
bartcharbon
closed
1 year ago
0
Update apptainer cmd for vip-report 5.4.0
#399
bartcharbon
closed
1 year ago
0
Bump vip-report to 5.4.0
#398
bartcharbon
closed
1 year ago
0
CuteSV workarounds - part I
#397
bartcharbon
closed
1 year ago
0
Fix #389 samtools markdup can fail
#396
dennishendriksen
closed
1 year ago
0
Fix awk command in annotSV workaround
#395
bartcharbon
closed
1 year ago
0
Expansion hunter
#394
dennishendriksen
closed
1 year ago
0
Change order of GnomadAF and AnnotSv in default tree
#393
bartcharbon
closed
1 year ago
0
Fix #391 concat_vcf input file name collision
#392
dennishendriksen
closed
1 year ago
0
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