Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
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Tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.


  • 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.


Clone and install regtools by running:

    git clone
    cd regtools/
    mkdir build
    cd build/
    cmake ..

For convienience we also maintain a docker image available at


    regtools --help


  • Issue Tracker:
  • Source Code:


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


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.


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.