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HAPGEN is a program thats simulates case control datasets at SNP markers and can output data in the FILE FORMAT used by IMPUTE, SNPTEST and GTOOL. The approach can handle markers in LD and can simulate datasets over large regions such as whole chromosomes. Hapgen simulates haplotypes by conditioning on a set of population haplotypes and an estimate of the fine-scale recombination rate across the region.
Command line syntax example for HAPGEN can be found by clicking here.
Project website: https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html
Load SGE module
The HAPGEN environment module can be loaded as follows
module load hapgen/hapgen