GenotypeHarmonizer¶

Description¶

The Genotype Harmonizer is an easy to use command-line tool that allows harmonization of genotype data stored using different file formats with different and potentially unknown strands.

Note: export _JAVA_OPTIONS="-Xmx?g" where ? equals to the available memory.

Environment Modules¶

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

Environment Variables¶

HPC_GENOTYPEHARMONIZER_DIR - installation directory
HPC_GENOTYPEHARMONIZER_BIN - executable directory
HPC_GENOTYPEHARMONIZER_DOC - documentation directory
HPC_GENOTYPEHARMONIZER_EXE - example directory

Citation¶

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

Deelen, P., Bonder, M. J., van der Velde, K. J., Westra, H.-J., Winder, E., Hendriksen, D., Franke, L., & Swertz, M. A. (2014). Genotype Harmonizer: Automatic strand alignment and format conversion for genotype data integration. BMC Research Notes, 7, 901. https://doi.org/10.1186/1756-0500-7-901

Categories¶

biology