molgenis / vip

Variant Interpretation Pipeline

https://molgenis.github.io/vip/

molgenis/vip Issues

Non-deterministic consequence annotations
Updated a day ago
ncER GRCh38 data contains overlapping values
Updated 3 months ago
Add AlphaMissense to annotations
Closed 6 months ago1
VIP errors if 2 filenames in the input are identical
Updated 8 months ago
filter samples somehow removes some INFO headers
Updated 8 months ago
Error merging SVs: The REF prefixes differ: A vs N (1,1)
Updated 6 months ago1
`nf-cram_str_straglr_call` can produce unsorted `vcf`
Closed 8 months ago
Report crashed in detail view for long read data (reads to big for genome browser)
Closed 9 months ago1
cuteSV can fail based on `~` content on host machine
Closed 10 months ago
Support .sam input in addition to .bam and .cram
Closed 10 months ago
Report can contain data of samples not in sample sheet
Closed 10 months ago
VCF index not created with HTSlib doesn't work
Closed 10 months ago
Succesfull pipeline execution if `individual_id` doesn't exist in vcf
Closed 10 months ago
`annotate` can fail with 'Failed to instantiate plugin GADO'
Closed 10 months ago1
`clair3_call` can fail with 'Chromosome blocks not continuous' error
Closed 10 months ago
`clair3 call` can fail due to cram-to-bam slice-and-convert issue
Closed 10 months ago
Project samples must have same assembly and sequencing_method
Closed 10 months ago
SV calling cannot detect translocations due to chunking
Closed 10 months ago
Multi-project slice called too many times
Closed 10 months ago
Multi-project getProbands, getHpoIds, createPedigree incorrect
Closed 10 months ago
Chromosome blocks not continuous error in cram workflow
Closed 10 months ago1
Error if .cram doesn't contain reads for a chunk
Closed 10 months ago
Process `cram:concat_vcf` input file name collision
Closed a year ago
samtools markdup failure
Closed a year ago
Sniffles produces invalid and malformed VCF
Closed a year ago
fastq/cram workflows do not validate params of subworkflows
Closed a year ago
out-of-memory error annotating one SV with `--custom` bigwig
Closed a year ago
gVCF merge fails for haploid calls
Closed a year ago2
VEP out-of-memory error annotating some long SVs
Closed a year ago
AnnotSV annotations missing or invalid
Closed a year ago
"Query asks for data past end of contig" during report creation
Closed a year ago2
`merge_vcf` proces can fail with GLnexus merge error
Closed a year ago
`build.sh` only works if ran from script directory
Closed 6 months ago
`install.sh` skips unfinished downloads
Closed 6 months ago1
Cram workflow can fail in case of 'B' nucleotide in reference
Closed a year ago
vips script return vip: line 93: args: readonly variable
Closed a year ago4
param --resume not working
Closed a year ago
vip.sh doesn't exit if config file does not exist
Closed a year ago
params.vcf.report.template validation error
Closed a year ago
gnomAD GRCh37 homozygous count doesn't include exomes
Closed a year ago1
AnnotSV doesn't work for GRCh38
Closed a year ago1
Invalid output when chunks exist with and without AnnotSV annotations
Closed a year ago
Nextflow does not abort pipeline run on VEP plugin failure
Closed a year ago1
VIP expects that GATK was used to call variants
Closed a year ago1
Hpo plugin broken
Closed 2 years ago
Artifact plugin broken
Closed 2 years ago
--filter_classes fails for single class
Closed 2 years ago
VIP install with different VEP assembly or version doesn't work
Closed 2 years ago
VIP install after update with new AnnotSV doesn't install new AnnotSV
Closed 2 years ago
VIP install might throw `gzip: stdin: not in gzip format` error
Closed 6 months ago1