https://github.com/molgenis/vip
Variant Interpretation Pipeline
https://github.com/molgenis/vip
genetics pipeline variant-interpretation
Last synced: 6 months ago
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Variant Interpretation Pipeline
- Host: GitHub
- URL: https://github.com/molgenis/vip
- Owner: molgenis
- License: lgpl-3.0
- Created: 2020-08-17T06:22:34.000Z (about 5 years ago)
- Default Branch: main
- Last Pushed: 2025-04-09T09:53:32.000Z (6 months ago)
- Last Synced: 2025-04-10T08:17:04.305Z (6 months ago)
- Topics: genetics, pipeline, variant-interpretation
- Language: Shell
- Homepage: https://molgenis.github.io/vip/
- Size: 514 MB
- Stars: 24
- Watchers: 6
- Forks: 6
- Open Issues: 14
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Variant Interpretation Pipeline
VIP is a flexible human variant interpretation pipeline for rare disease using state-of-the-art pathogenicity
prediction ([CAPICE](https://github.com/molgenis/capice)) and template-based interactive reporting to facilitate
decision support.
## Documentation
VIP documentation is available at this link https://molgenis.github.io/vip/.
> [!TIP]
> Visit https://vip.molgeniscloud.org/ to analyse your own variants
> [!TIP]
> Preprint now available at medRxiv
## Quick Reference
### Requirements
- [GNU-based Linux](https://en.wikipedia.org/wiki/Linux_distribution#Widely_used_GNU-based_or_GNU-compatible_distributions) (
e.g. Ubuntu, [Windows Subsystem for Linux](https://learn.microsoft.com/en-us/windows/wsl/about))
with [x86_64](https://en.wikipedia.org/wiki/X86-64) architecture
- Bash ≥ 3.2
- Java ≥ 11
- [Apptainer](https://apptainer.org/docs/admin/main/installation.html#install-from-pre-built-packages) (setuid
installation)
- 8GB RAM (an estimate, see also the [documentation](https://molgenis.github.io/vip/get_started/requirements/))
- 280GB disk space
### Installation
#### Default
```bash
curl -sSL https://download.molgeniscloud.org/downloads/vip/install.sh | bash
```
#### EasyBuild
HPC systems running [EasyBuild](https://easybuild.io/) can install VIP by adapting the `/apps` paths in
the [easyconfig files](https://github.com/molgenis/take-it-easyconfigs/tree/main/v/vip) to your local environment.
### Usage
```bash
usage: vip.sh -w -i -o
-w, --workflow workflow to execute. allowed values: cram, fastq, gvcf, vcf
-i, --input path to sample sheet .tsv
-o, --output output folder
-c, --config path to additional nextflow .cfg (optional)
-p, --profile nextflow configuration profile (optional)
-r, --resume resume execution using cached results (default: false)
-s, --stub quickly prototype workflow logic using process script stubs
-h, --help print this message and exit
```
## Developers
To create the documentation pages:
```
pip install mkdocs mkdocs-mermaid2-plugin
mkdocs serve
```
### License
VIP is an aggregate work of many works, each covered by their own licence(s). For the purposes of determining what you
can do with specific works in VIP, this policy should be read together with the licence(s) of the relevant tools. For
the avoidance of doubt, where any other licence grants rights, this policy does not modify or reduce those rights under
those licences.