RegTools
RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context. You can find the source code at our GitHub repository or just use our Docker image without need for installation.
Features
- Extract exon-exon junctions from a RNAseq BAM/CRAM 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:
git clone https://github.com/griffithlab/regtools
cd regtools/
mkdir build
cd build/
cmake ..
make
Usage
regtools --help
For information about the individual RegTools commands, please see the Commands page
Contribute
Citation
You can find a bioRxiv preprint describing our intial validation of RegTools here
Support
If you have issues using the project, please let us know. We have a mailing list located at: regtools@googlegroups.com and the forum is here. Another options is to use our GitHub issues page to contact the project about potential bugs.
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.