Gangstr

Introduction

GangSTR is a tool for genome-wide profiling tandem repeats from short reads. A key advantage of GangSTR over existing genome-wide TR tools (e.g. lobSTR or hipSTR) is that it can handle repeats that are longer than the read length. GangSTR takes aligned reads (BAM) and a set of repeats in the reference genome as input and outputs a VCF file containing genotypes for each locus.

For more information, please check:

BioContainers: https://biocontainers.pro/tools/gangstr

Home page: https://github.com/gymreklab/GangSTR

Versions

• 2.5.0

Commands

• GangSTR

Module

You can load the modules by:

module load biocontainers
module load gangstr

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 gangstr on our clusters:

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

module --force purge
ml biocontainers gangstr