Vcftools

vcftools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project.[1]

Installed Versions

Use one of the modulefiles:

vcftools/20170217 vcftools/20170911

N.B. The newer vcftools/20170911 is multithreaded for possible performance improvement.

Running

Some of the vcftools are multithreaded, so request the shm PE. See Writing_Job_Scripts#Parallel_Environment_.28PE.29

Compiling

Modules

Load these modules:

* zlib/cloudflare/gcc/1.2.8
* perl-threaded
* proteus-blas/gcc/64/20110419
* proteus-lapack/gcc/64/3.5.0

Configure and Make

Fairly straightforward. Instructions at the website: https://vcftools.github.io/examples.html

export CXXFLAGS="-O3 -march=corei7-avx -pthread"
export CPPFLAGS="-DBGZF_MT -I${ZLIBINC}"
export LDFLAGS="-Wl,-rpath,${ZLIBDIR} -Wl,-rpath,${LAPACKLIBDIR} -Wl,-rpath,${BLASLIBDIR}"
export LIBS="-llapack -lblas -lz"

./configure --prefix=/mnt/HA/groups/myrsrchGrp --enable-largefile --enable-pca
make

References

[1] VCFtools website