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vcftools website  

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. Upstream documentation for vcftools.

Required Modules

modules documentation


  • vcftools

System Variables

  • HPC_VCFTOOLS_DIR - installation directory
  • HPC_VCFTOOLS_BIN - executable directory

How To Run

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 /ufrc 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}


If you publish the research that uses this software please cite The Variant Call Format and VCFtools, Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert Handsaker, Gerton Lunter, Gabor Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin and 1000 Genomes Project Analysis Group, Bioinformatics, 2011.