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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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Process `cram:concat_vcf` input file name collision
#391
dennishendriksen
closed
1 year ago
0
Update VKGL, ClinVar, Inheritance, HPO, AnnotSV
#390
dennishendriksen
closed
1 year ago
0
samtools markdup failure
#389
dennishendriksen
closed
1 year ago
0
Sniffles produces invalid and malformed VCF
#388
dennishendriksen
closed
1 year ago
0
Fix #386 fastq/cram workflows do not validate params of subworkflows
#387
dennishendriksen
closed
1 year ago
0
fastq/cram workflows do not validate params of subworkflows
#386
dennishendriksen
closed
1 year ago
0
out-of-memory error annotating one SV with `--custom` bigwig
#385
dennishendriksen
closed
1 year ago
0
Fix #385 VEP out-of-memory workaround: replace bigWig with bed
#384
dennishendriksen
closed
1 year ago
0
Rank genes based on a patient’s phenotypes using GADO
#383
dennishendriksen
closed
1 year ago
0
Fix #388 Replace Sniffles2 with cuteSV
#382
dennishendriksen
closed
1 year ago
0
Validate vcf after clair3 run
#381
bartcharbon
closed
1 year ago
0
Fix: Publish vcf with all chunks instead of one chunk
#380
bartcharbon
closed
1 year ago
0
docs:update sample classification tree
#379
dennishendriksen
closed
1 year ago
0
Classify proband ref/ref variant-effects as HR
#378
dennishendriksen
closed
1 year ago
0
fix:bump vcf-decision-tree 3.5.3 to 3.5.4
#377
dennishendriksen
closed
1 year ago
0
Update vip-report version to v5.3.0
#376
bartcharbon
closed
1 year ago
0
Bump CrossMap 0.6.1 to 0.6.5
#375
dennishendriksen
closed
1 year ago
0
Bump Seqtk 1.3 to 1.4
#374
dennishendriksen
closed
1 year ago
0
Update Clair3 v1.0.1 to v1.0.2
#373
dennishendriksen
closed
1 year ago
0
Throw informative error in case of chromosome mismatch
#372
dennishendriksen
closed
1 year ago
0
Update glnexus from 1.4.1 to 1.4.5-patched
#371
dennishendriksen
closed
1 year ago
0
gVCF merge fails for haploid calls
#370
dennishendriksen
closed
1 year ago
2
Replace VEP "error grep" with "--safe"
#369
bartcharbon
closed
1 year ago
0
Fix #367 Workaround for VEP out-of-memory errors
#368
dennishendriksen
closed
1 year ago
0
VEP out-of-memory error annotating some long SVs
#367
dennishendriksen
closed
1 year ago
0
Feat/annot sv p ass
#366
bartcharbon
closed
1 year ago
1
Bump Clair3 v1.0.0 to v1.0.1
#365
dennishendriksen
closed
1 year ago
0
bump vcf-inheritance 3.1.0 to 3.1.2
#364
dennishendriksen
closed
1 year ago
0
Add cram nanopore test
#363
bartcharbon
closed
1 year ago
0
gvcf_merge_preset 'gatk_unfiltered' and set to default
#362
dennishendriksen
closed
1 year ago
0
Fix #360 AnnotSV annotations missing or invalid
#361
dennishendriksen
closed
1 year ago
0
AnnotSV annotations missing or invalid
#360
dennishendriksen
closed
1 year ago
0
Workaround for Ensembl/ensembl-vep#1397
#359
dennishendriksen
closed
1 year ago
0
Update dependencies
#358
dennishendriksen
closed
1 year ago
0
Fail VIP on failure of VEP plugin
#357
bartcharbon
closed
1 year ago
0
Replace CMD env variables with params (WfExS compatibility)
#356
dennishendriksen
closed
1 year ago
1
vcf multiproject classify test runs local
#355
bartcharbon
closed
1 year ago
0
Publish vcf result from cram workflow
#354
bartcharbon
closed
1 year ago
0
Update requirements.md
#353
dennishendriksen
closed
1 year ago
0
fix:SAMtools can connect to EBI
#352
dennishendriksen
closed
1 year ago
0
"Query asks for data past end of contig" during report creation
#351
dennishendriksen
closed
1 year ago
2
samtools_addreplacerg: reduce intermediate files
#350
dennishendriksen
closed
1 year ago
0
Fix inheritance: add option to provide genemap2
#349
bartcharbon
closed
1 year ago
0
fix:reheader workaround
#348
dennishendriksen
closed
1 year ago
0
Reduce chunk size to size of largest contig
#347
dennishendriksen
closed
1 year ago
1
Fix #344 merge_vcf proces can fail with GLnexus merge error
#346
dennishendriksen
closed
1 year ago
0
Bump clair to V1 and remove workaround IUPAC
#345
bartcharbon
closed
1 year ago
0
`merge_vcf` proces can fail with GLnexus merge error
#344
dennishendriksen
closed
1 year ago
0
fix:only allow sudo for 'apptainer build'
#343
dennishendriksen
closed
1 year ago
0
fix:remove call to undefined stats function in sniffles2_call.sh
#342
dennishendriksen
closed
1 year ago
0
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