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/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.
Clone and install regtools by running:
git clone https://github.com/griffithlab/regtools cd regtools/ mkdir build cd build/ cmake .. make
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.
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
For information about the individual RegTools commands, please see the Commands page
You can find a bioRxiv preprint describing our intial validation of RegTools here
If you have issues using the project, please let us know. We have a mailing list located at: email@example.com and the forum is here. Another options is to use our GitHub issues page 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.