impute2
Link to section 'Introduction' of 'impute2' Introduction
Impute2 is a genotype imputation and haplotype phasing program.
For more information, please check its website: https://biocontainers.pro/tools/impute2 and its home page: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#home.
Link to section 'Versions' of 'impute2' Versions
- 2.3.2
Link to section 'Commands' of 'impute2' Commands
- impute2
Link to section 'Module' of 'impute2' Module
You can load the modules by:
module load biocontainers
module load impute2
Link to section 'Example job' of 'impute2' Example job
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 -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=impute2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers impute2
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