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

If one wishes to test their installation, we include test data under tests/integration-test/data.

Here's an example command using that data along with the example output.

regtools cis-splice-effects identify -s RF tests/integration-test/data/vcf/test1.vcf tests/integration-test/data/bam/test_hcc1395.2.bam tests/integration-test/data/fa/test_chr22.fa tests/integration-test/data/gtf/test_ensemble_chr22.2.gtf

chrom   start   end name    score   strand  splice_site acceptors_skipped   exons_skipped   donors_skipped  anchor  known_donor known_acceptor  known_junction  gene_names  gene_ids    transcripts variant_info
22  93668   97252   JUNC00000001    5   +   GT-AG   1   1   1   NDA 1   1   0   EP300   ENSG00000100393 ENST00000263253 22:94626-94627

For information about the individual RegTools commands, please see the Commands page

Contribute

Citation

Cotto KC, Feng YY, Ramu A, Richters M, Freshour SL, Skidmore ZL, Xia H, McMichael JF, Kunisaki J, Campbell KM, Chen TH, Rozycki EB, Adkins D, Devarakonda S, Sankararaman S, Lin Y, Chapman WC, Maher CA, Arora V, Dunn GP, Uppaluri R, Govindan R, Griffith OL, Griffith M. Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer. Nature Communications. 2023 Mar. pmid: 36949070; doi: 10.1038/s41467-023-37266-6

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.