Shapeit4

Introduction

SHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and high coverage sequencing data.

For more information, please check:

BioContainers: https://biocontainers.pro/tools/shapeit4

Home page: https://odelaneau.github.io/shapeit4/

Versions

• 4.2.2

Commands

• shapeit4

Module

You can load the modules by:

module load biocontainers
module load shapeit4

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 shapeit4 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=shapeit4
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers shapeit4