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.
RegTools requires only a standard computer with enough RAM to support the in-memory operations.
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
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/
If one wishes to test their installation, we include test data under
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
- Issue Tracker: github.com/griffithlab/regtools/issues
- Source Code: github.com/griffithlab/regtools
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 - https://groups.google.com/forum/#!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
pip install mkdocs --user should
work on most machines. Then run
mkdocs serve from within the
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.