Software: RNAIndel
Description
RNAIndel calls coding indels from tumor RNA-Seq data and classifies them as somatic, germline, and artifactual. RNAIndel supports GRCh38 and 37.
Available Versions
| Unspecified: | 3.0.9 |
|---|
For more information, please check its Github package: https://github.com/stjude/RNAIndel/pkgs/container/rnaindel and its home page on Github.
Commands
- rnaindel
Module
You can load the modules by:
module load biocontainers
module load rnaindel
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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