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These inputs are at least partially described in the GCTA documentation here. An example of the causal.snplist is given as a 2-column file with causal SNPs and effect sizes. No description of the test.indi.list is given but it is described elsewhere as merely a list of individual IDs to use in the analysis. If you continue experiencing difficulties you ...


It is described with respect to the reference sequence. See the VCF format description.

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