VCFtools

Overview

VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide methods for working with VCF files: validating, merging, comparing and calculate some basic population genetic statistics.

Version 0.1.14 is installed on the CSF. It was compiled with gcc 4.9.0. There is a version 0.1.14 which uses zlib 1.2.8 which may give better performance.

Version 0.1.11 is also installed on the CSF. It was compiled with gcc 4.7.0.

Restrictions on use

The software is open source. All CSF users may access it.

Set up procedure

To access the software you must first load the appropriate modulefile:

module load apps/gcc/vcftools/0.1.14-zlib1.2.8

module load apps/gcc/vcftools/0.1.14

OR

module load apps/gcc/vcftools/0.1.11

Running the application

Please do not run VCFtools on the login node. Jobs should be submitted to the compute nodes via batch.

Serial batch job submission

Coming soon.

Parallel batch job submission

Coming soon.

Further info

• VCFtools website

Updates