Biowulf High Performance Computing at the NIH
Vcftools on Biowulf

VCFtools contains a Perl API ( and a number of Perl scripts that can be used to perform common tasks with VCF files such as file validation, file merging, intersecting, complements, etc. The Perl tools support all versions of the VCF specification (3.2, 3.3, and 4.0), nevertheless, the users are encouraged to use the latest version VCFv4.0. The VCFtools in general have been used mainly with diploid data, but the Perl tools aim to support polyploid data as well.

VCFTools is maintained and developed by Adam Auton, Peter Danecek and collaborators.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

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 vcftools
[user@cn3144 ~]$ compare-vcf inputFile1 inputFile2

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

Batch job
Most jobs should be run as batch jobs.

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

set -e
module load vcftools
compare-vcf inputFile1 inputFile2

Submit this job using the Slurm sbatch command.

sbatch --mem=10g
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

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

cd dir1;compare-vcf inputFile1 inputFile2
cd dir2;compare-vcf inputFile1 inputFile2
cd dir3;compare-vcf inputFile1 inputFile2
cd dir4;compare-vcf inputFile1 inputFile2
cd dir5;compare-vcf inputFile1 inputFile2

Submit this job using the swarm command.

swarm -f vcftools.swarm -g 10 --module vcftools
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module vcftools Loads the fastqc module for each subjob in the swarm