RNAIndel

Introduction

RNAIndel calls coding indels from tumor RNA-Seq data and classifies them as somatic, germline, and artifactual. RNAIndel supports GRCh38 and 37.

For more information, please check its Github package: https://github.com/stjude/RNAIndel/pkgs/container/rnaindel and its home page on Github.

Versions

3.0.9

Commands

rnaindel

Module

You can load the modules by:

module load biocontainers
module load rnaindel

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run RNAIndel on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=rnaindel
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers rnaindel