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.
- 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.
Clone and install regtools by running:
git clone https://github.com/griffithlab/regtools cd regtools/ mkdir build cd build/ cmake .. make
For information about the individual regtools commands, please see the Commands page
If you have issues using the project, please let us know. We have a mailing list located at: firstname.lastname@example.org and the forum is here. Github issues are another option to contact the project about potential bugs.
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.
The project is licensed under the MIT license.