RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.

References:

• Cotto, K.C., Feng, YY., Ramu, A. et al. RegTools: Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer Nat Commun 14, 1589 (2023)

• Regtools Main Site
• Regtools Github Site

• Module Name: regtools (see the modules page for more information)
• Environment variables set
  • REGTOOLS_HOME
• Example files in /usr/local/apps/regtools/1.0.0/regtools/test-data

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
[user@cn4338 ~]$ module load regtools
[+] Loading regtools 1.0.0  on cn4338 
[+] Loading singularity  3.10.5  on cn4338

Running help command:

[user@cn4338] cp -a /usr/local/apps/regtools/1.0.0/regtools/test-data .
[user@cn4338 test-data]$ regtools --help
Program:        regtools
Version:        1.0.0
Usage:          regtools  [options]
Command:        junctions               Tools that operate on feature junctions (e.g. exon-exon junctions from RNA-seq).
                cis-ase                 Tools related to allele specific expression in cis.
                cis-splice-effects      Tools related to splicing effects of variants.
                variants                Tools that operate on variants.

Create a batch input file (e.g. regtools.sh). For example:

#!/bin/bash
module load regtools

regtools cis-splice-effects identify -s FR variants.vcf alignments.bam ref.fa annotations.gtf

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] regtools.sh

cis-splice-effects:

[user@cn4338 test-data]$
  regtools cis-splice-effects identify -s RF \
   test4.vcf.gz \
   test_hcc1395.bam \
   test_chr22.fa \
   test_ensemble_chr22.gtf

  Program:        regtools
  Version:        1.0.0
  Variant file: test4.vcf.gz
  Alignment file: test_hcc1395.bam
  Reference fasta file: test_chr22.fa
  Annotation file: test_ensemble_chr22.gtf
  
  exonic_min_distance_ is 3
  
  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