Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Create a feature comparison matrix for mehari #425

Open
xiamaz opened this issue Mar 29, 2024 · 2 comments
Open

Create a feature comparison matrix for mehari #425

xiamaz opened this issue Mar 29, 2024 · 2 comments
Labels
enhancement New feature or request

Comments

@xiamaz
Copy link
Contributor

xiamaz commented Mar 29, 2024

Is your feature request related to a problem? Please describe.
Currently it is not clear how mehari compares feature-wise to other available solutions.

Describe the solution you'd like
Identify all publicly available variant annotation software and create a feature comparison for the most important ones.

Describe alternatives you've considered
...

Additional context
Result should be an artifact in docs.

@xiamaz xiamaz added the enhancement New feature or request label Mar 29, 2024
@xiamaz
Copy link
Contributor Author

xiamaz commented Mar 29, 2024

software url language features
AnnoVar https://annovar.openbioinformatics.org/en/latest/ perl
SnpEff https://pcingola.github.io/SnpEff/ java
VEP https://www.ensembl.org/info/docs/tools/vep/index.html perl plugin system
Jannovar https://github.com/charite/jannovar/ java inheritance annotation, vcf/position/vcf/hgvs input, variant normalization
open-cravat https://github.com/KarchinLab/open-cravat?tab=readme-ov-file python custom primary transcripts, plugin system
nirvana https://github.com/Illumina/Nirvana C# json output only, custom annotations, mnv recomposition, fusion gene detection

@xiamaz
Copy link
Contributor Author

xiamaz commented Mar 29, 2024

Candidates for benchmarking:

nirvana, jannovar, VEP, open-cravat

@xiamaz xiamaz moved this to In progress in Release Planning May 29, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
Status: In progress
Development

No branches or pull requests

1 participant