OpenCRAVAT
Install via pip
OpenCRAVAT is a versatile tool for variant annotation and analysis. You can easily install it using Python’s package manager, pip. Use the command below to get OpenCRAVAT up and running on your system:
python3 -m pip install open-cravat
Installers
The OpenCRAVAT installer provides a user-friendly setup process, allowing users to easily install the software with a few clicks. It includes all necessary dependencies and offers an intuitive interface for variant annotation and analysis right out of the box.
BioConda
Bioconda is a cross-platform package manager and can be used as an alternative to pip when installing OpenCRAVAT.
SnakeMake
Snakemake is a Python-based workflow management system that evolved from the Unix Make utility. It enables seamless scaling of workflows from single-core workstations to servers, clusters, grids, and cloud environments without requiring changes to the workflow definition. Integrating OpenCRAVAT with Snakemake simplifies incorporating OpenCRAVAT into larger bioinformatics pipelines.
GenePattern
Running OpenCRAVAT with GenePattern notebooks offers a seamless way to annotate and analyze genetic variants. GenePattern notebooks provide an interactive, user-friendly environment that supports reproducible research. This integration enables researchers to annotate variants, customize workflows, directly work with data in code, visualize results interactively, and share analyses with collaborators.
Docker
OpenCRAVAT is available as a Docker container (with over 50,000 downloads!). All functionality is available in the container, including command-line annotation, high-throughput VCF annotation, and the OpenCRAVAT GUI. Designed for highly parallel annotation in the cloud and incorporation into large bioinformatics pipelines.
