MERLIN uses sparse trees to represent gene flow in pedigrees and is one of the fastest pedigree analysis packages around (Abecasis et al, 2002).

• http://www.sph.umich.edu/csg/abecasis/Merlin/tour/linkage.html

• Module Name: merlin (see the modules page for more information)
• Example files: /usr/local/apps/merlin/version/examples/

Allocate an interactive session and run the program. Sample session:

[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 merlin
[user@cn3144 ~]$ merlin -d x.dat -p x.ped -m x.map

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

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

#!/bin/bash
set -e
module load merlin
merlin -d x.dat -p x.ped -m x.map

Submit this job using the Slurm sbatch command.

sbatch batch.sh

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

cd dir1; merlin -d x.dat -p x.ped -m x.map
cd dir2; merlin -d x.dat -p x.ped -m x.map
cd dir3; merlin -d x.dat -p x.ped -m x.map

Submit this job using the swarm command.

swarm -f job.swarm --module merlin