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PLINK/SEQ on Biowulf & Helix

PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing projects, particularly whole-exome and whole-genome studies. However, the library could in principle be applied to other types of genetic studies, including whole-genome association studies of common SNPs.

Plink/Seq was developed at Harvard University

Running on Helix

$ module load plinkseq
$ cd /data/$USER/dir
$ pseq ex1.vcf v-view --vmeta --gmeta

Running a single batch job on Biowulf

1. Create a script file. The file will contain the lines similar to the lines below.

#!/bin/bash


module load plinkseq
cd /data/$USER/dir
pseq ex1.vcf v-view --vmeta --gmeta

2. Submit the script on biowulf:

$ sbatch jobscript

If more momory is required (default 4gb), specify --mem=Mg, for example --mem=10g:

$ sbatch --mem=10g jobscript

Running a swarm of jobs on Biowulf

Setup a swarm command file:

  cd /data/$USER/dir1; pseq ex1.vcf v-view --vmeta --gmeta
  cd /data/$USER/dir2; pseq ex1.vcf v-view --vmeta --gmeta
  cd /data/$USER/dir3; pseq ex1.vcf v-view --vmeta --gmeta
	[......]
  

Submit the swarm file, -f specify the swarmfile name, and --module will be loaded the required module for each command line in the file:

  $ swarm -f swarmfile --module plinkseq

If more memory is needed for each line of commands, the below example allocate 10g for each command:

  $ swarm -f swarmfile -g 10 --module plinkseq

For more information regarding running swarm, see swarm.html

Running an interactive job on Biowulf

It may be useful for debugging purposes to run jobs interactively. Such jobs should not be run on the Biowulf login node. Instead allocate an interactive node as described below, and run the interactive job there.

biowulf$ sinteractive 
salloc.exe: Granted job allocation 16535

cn999$ module load plinkseq
cn999$ cd /data/$USER/dir
cn999$ pseq ex1.vcf v-view --vmeta --gmeta
[...etc...]

cn999$ exit
exit

biowulf$

Make sure to exit the job once finished.

If more memory is needed, use --mem. For example

biowulf$ sinteractive --mem=8g

Documentation

http://atgu.mgh.harvard.edu/plinkseq/