HAPGEN: Difference between revisions
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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. | [https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html 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 [ | Command line syntax example for HAPGEN can be found by [https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html#Running_HAPGEN_top clicking here]. | ||
The HAPGEN environment module can be loaded as follows | The HAPGEN environment module can be loaded as follows | ||
<pre> | <pre> | ||
module load hapgen/hapgen | module load hapgen/hapgen | ||
</pre> | </pre> | ||
Revision as of 15:46, 20 March 2012
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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.
The HAPGEN environment module can be loaded as follows
module load hapgen/hapgen