Impute2 is a genotype imputation and haplotype phasing program.
For more information, please check:
BioContainers: https://biocontainers.pro/tools/impute2
- 2.3.2
- impute2
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