vcftools¶

Description¶

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.

Environment Modules¶

Run module spider vcftools to find out what environment modules are available for this application.

Environment Variables¶

HPC_VCFTOOLS_DIR - installation directory
HPC_VCFTOOLS_BIN - executable directory

Additional Usage Information¶

By default vcftools uses /tmp for temporary file storage. As explained in vcftools documentation you should use the --temp argument to point vcftools to a directory in your /blue space instead since HiPerGator2 nodes are diskless and the /tmp directory on them is very small. For example, the following can be used in a job script:

mkdir -p tmp
export TMPDIR="$(pwd)/tmp"

vcftools ... --temp ${TMPDIR}

Citation¶

If you publish research that uses vcftools you have to cite it as follows:

Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G., Marth, G. T., Sherry, S. T., McVean, G., Durbin, R., & 1000 Genomes Project Analysis Group. (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156-2158. https://doi.org/10.1093/bioinformatics/btr330

Categories¶

biology, genomics