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 test_data.

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

Contribute

• Issue Tracker
• Source Code

Citation

You can find a bioRxiv preprint describing our intial validation of RegTools here

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.