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Joyvalley / GWAS_Flow

GPU accelerated GWAS framework based on TensorFlow
MIT License
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Error in vanRaden kinship calculation #27

Closed iimog closed 2 years ago

iimog commented 2 years ago

There is an error in the implementation of the kinship matrix after vanRaden. Column i of p_mat should be 2 * (p_i - 0.5). In addition the coding of the genotype matrix might be incorrect for vanRaden (requires {-1,0,1} receives {0, 0.5, 1}). https://github.com/Joyvalley/GWAS_Flow/blob/cafa4d71bbc2363f26a27597234ef3dc0155b25f/gwas_flow/main.py#L16

Originally reported by Maura John

iimog commented 2 years ago

It was always recommended to provide a proper kinship matrix. So starting from version 1.2.0 this is required.