griffithlab/regtools repository overview

⁠regtools

Tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.

⁠Features

• Identify evidence for aberrant splicing in RNA reads near a list of variants.
• Extract exon-exon junctions from a RNAseq BAM file.
• Annotate exon-exon junctions with information from a known transcriptome.
• Annotate variants with splice-region(the definition of this region is configurable) annotations.

⁠Installation

Clone and install regtools by running the following:

    git clone https://github.com/griffithlab/regtools
    cd regtools/
    mkdir build
    cd build/
    cmake ..
    make

For convienience we also maintain a docker image available at https://hub.docker.com/r/griffithlab/regtools/⁠

⁠Usage:

    regtools --help

⁠Contribute

• Issue Tracker: github.com/griffithlab/regtools/issues
• Source Code: github.com/griffithlab/regtools

⁠Support

If you have issues using the project, please let us know. We have a mailing list located at: [email protected]⁠ and the forum is here - https://groups.google.com/forum/#!forum/regtools⁠. Github issues are another option to contact the project about potential bugs.

⁠Documentation

The documentation for the project is hosted on Read the Docs.⁠

If you would like to build the documentation locally, please install mkdocs⁠, pip install mkdocs --user should work on most machines. Then run mkdocs serve from within the regtools base directory.

⁠Acknowledgements

Regtools uses several open-source libraries. We would like to thank the developers of htslib and bedtools. We would also like to thank Travis Abbott for useful comments and code.

⁠License

The project is licensed under the MIT license⁠.

⁠Stable release with DOI