Impute2

Introduction

Impute2 is a genotype imputation and haplotype phasing program.

For more information, please check:

BioContainers: https://biocontainers.pro/tools/impute2

Home page: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#home

Versions

• 2.3.2

Commands

• impute2

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 impute2 on our clusters:

#!/bin/bash
#SBATCH -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=impute2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load impute2/XXXX ### you can run *module avail impute2* to check all available versions

impute2 \
        -m Example/example.chr22.map \
        -h Example/example.chr22.1kG.haps \
        -l Example/example.chr22.1kG.legend \
        -g Example/example.chr22.study.gens \
        -strand_g Example/example.chr22.study.strand \
        -int 20.4e6 20.5e6 \
        -Ne 20000 \
        -o example.chr22.one.phased.impute2