When genotype values are not in 0.0-2.0 range no error is reported and MAF filter is wrong

genetics-statistics / GEMMA

Genome-wide Efficient Mixed Model Association

https://github.com/genetics-statistics/GEMMA

GNU General Public License v3.0

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When genotype values are not in 0.0-2.0 range no error is reported and MAF filter is wrong #187

Closed pjotrp closed 5 years ago

pjotrp commented 6 years ago

According to manual genotype values 0.0-2.0 should be used. In the example BXD files values range from 0.0-1.0 and no error is reported. I don't think it hurts GWA per se, but MAF values will be wrong and therefore the results may be a bit off.

A fix should also address #184.