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.

Hardware requirements

RegTools requires only a standard computer with enough RAM to support the in-memory operations.

Software requirements

OS Requirements This package is supported for macOS and Linux. The package has been tested on the following systems:

macOS: macOS 10.12 (Sierra), macOS 10.13 (High Sierra), macOS 10.14 (Mojave), macOS 10.15 (Catalina), macOS 11 (Big Sur), macOS 12 (Monterey)

Linux: Ubuntu 16.04, Ubuntu 18.04, Ubuntu 20.04

Installation

Clone and install regtools by running the following:

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

Installation should take 1-5 minutes.

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

Usage:

    regtools --help

If one wishes to test their installation, we include test data under test_data.

Here’s an example command using that data along with the example output. This should run in under a minute.

regtools cis-splice-effects identify -s RF -e 10 -i 10 test_data/HCC1395_chr22.vcf.gz test_data/HCC1395_tumor.bam test_data/chr22_with_ERCC92.fa test_data/chr22_with_ERCC92.gtf

Variant 22    42129188    42129189    -1
Variant region is 22:42128784-42130813

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
position = 22:42125408-42125409
position = 22:42130565-42130566
22    42125407    42130567    JUNC00000001    4    +    GT-AG    0    0    0    D    1    0    0    NDUFA6-AS1    ENSG00000237037    ENST00000439129    22:42129188-42129189
position = 22:42128881-42128882
position = 22:42129670-42129671
22    42128880    42129672    JUNC00000002    3    +    GT-AG    0    0    0    N    0    0    0    NA    NA    NA    22:42129188-42129189
position = 22:42128944-42128945
position = 22:42129031-42129032
22    42128943    42129033    JUNC00000003    4    -    GT-GG    1    0    0    D    1    0    0    CYP2D6    ENSG00000100197    ENST00000360608,ENST00000389970,ENST00000488442    22:42129188-42129189
position = 22:42129783-42129784
position = 22:42143453-42143454
22    42129782    42143455    JUNC00000004    2    +    GC-AG    9    8    9    N    0    0    0    NA    NA    NA    22:42129188-42129189
position = 22:42130224-42130225
position = 22:42130565-42130566
22    42130223    42130567    JUNC00000005    2    +    GT-AG    0    0    0    N    0    0    0    NA    NA    NA    22:42129188-42129189

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: regtools@googlegroups.com 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.