{"id":20189577,"url":"https://github.com/molgenis/vip","last_synced_at":"2025-04-10T08:28:06.901Z","repository":{"id":36955181,"uuid":"288100002","full_name":"molgenis/vip","owner":"molgenis","description":"Variant Interpretation 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Variant Interpretation Pipeline\n\nVIP is a flexible human variant interpretation pipeline for rare disease using state-of-the-art pathogenicity\nprediction ([CAPICE](https://github.com/molgenis/capice)) and template-based interactive reporting to facilitate\ndecision support.\n\n![Example Report](docs/img/report_example.png)\n\n## Documentation\n\nVIP documentation is available at this link https://molgenis.github.io/vip/.\n\n\u003e [!TIP]\n\u003e Visit \u003ca href=\"https://vip.molgeniscloud.org/\"\u003ehttps://vip.molgeniscloud.org/\u003c/a\u003e to analyse your own variants\n\n\u003e [!TIP]\n\u003e Preprint now available at \u003ca href=\"https://doi.org/10.1101/2024.04.11.24305656\"\u003emedRxiv\u003c/a\u003e\n\n## Quick Reference\n\n### Requirements\n\n- [GNU-based Linux](https://en.wikipedia.org/wiki/Linux_distribution#Widely_used_GNU-based_or_GNU-compatible_distributions) (\n  e.g. Ubuntu, [Windows Subsystem for Linux](https://learn.microsoft.com/en-us/windows/wsl/about))\n  with [x86_64](https://en.wikipedia.org/wiki/X86-64) architecture\n- Bash ≥ 3.2\n- Java ≥ 11\n- [Apptainer](https://apptainer.org/docs/admin/main/installation.html#install-from-pre-built-packages) (setuid\n  installation)\n- 8GB RAM (an estimate, see also the [documentation](https://molgenis.github.io/vip/get_started/requirements/))\n- 280GB disk space\n\n### Installation\n\n#### Default\n\n```bash\ncurl -sSL https://download.molgeniscloud.org/downloads/vip/install.sh | bash\n```\n\n#### EasyBuild\n\nHPC systems running [EasyBuild](https://easybuild.io/) can install VIP by adapting the `/apps` paths in\nthe [easyconfig files](https://github.com/molgenis/take-it-easyconfigs/tree/main/v/vip) to your local environment.\n\n### Usage\n\n```bash\nusage: vip.sh -w \u003carg\u003e -i \u003carg\u003e -o \u003carg\u003e\n  -w, --workflow \u003carg\u003e  workflow to execute. allowed values: cram, fastq, gvcf, vcf\n  -i, --input    \u003carg\u003e  path to sample sheet .tsv\n  -o, --output   \u003carg\u003e  output folder\n  -c, --config   \u003carg\u003e  path to additional nextflow .cfg (optional)\n  -p, --profile  \u003carg\u003e  nextflow configuration profile (optional)\n  -r, --resume          resume execution using cached results (default: false)\n  -s, --stub            quickly prototype workflow logic using process script stubs\n  -h, --help            print this message and exit\n```\n\n## Developers\n\nTo create the documentation pages:\n\n```\npip install mkdocs mkdocs-mermaid2-plugin\nmkdocs serve\n```\n\n### License\n\nVIP is an aggregate work of many works, each covered by their own licence(s). For the purposes of determining what you\ncan do with specific works in VIP, this policy should be read together with the licence(s) of the relevant tools. For\nthe avoidance of doubt, where any other licence grants rights, this policy does not modify or reduce those rights under\nthose licences.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmolgenis%2Fvip","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmolgenis%2Fvip","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmolgenis%2Fvip/lists"}