Minimac is a low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation.

• Minimac4 website

• Module Name: minimac (see the modules page for more information)
• minimac-omp is multi-threaded. Plain 'minimac' is single-threaded.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load minimac
[+] Loading minimac minimac4  ...

[user@cn3144 ~]$  minimac4 --refHaps refPanel.vcf \ 
                --haps targetStudy.vcf \
                --prefix testRun

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. minimac.sh). For example:

#!/bin/bash
set -e
module load minimac/minimac4
minimac-omp --cpus $SLURM_CPUS_PER_TASK --refHaps refPanel.vcf \ 
                --haps targetStudy.vcf \
                --prefix testRun

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 [--mem=#] minimac.sh

Create a swarmfile (e.g. minimac.swarm). For example:

minimac-omp --cpus $SLURM_CPUS_PER_TASK -refHaps ref1.vcf --haps target1.vcf --prefix test1
minimac-omp --cpus $SLURM_CPUS_PER_TASK -refHaps ref2.vcf --haps target2.vcf --prefix test2
minimac-omp --cpus $SLURM_CPUS_PER_TASK -refHaps ref3.vcf --haps target3.vcf --prefix test3

Submit this job using the swarm command.

swarm -f minimac.swarm [-g #] [-t 4] --module minimac