Hi, I’m new to Hail. I would like to conduct GWAS (linear regression), however, the genotype data is stored in a HDF5 file. In the the HDF5 file, I have every sample’s allele count at each locus. I think it should be straight forward to use these allele counts to run GWAS in Hail. But I’m not sure: …

It’s not super easy to go directly from numpy => hail – it may be easier to go through a text intermediate and use hl.import_matrix_table .

Read HDF5 file and run GWAS

Liverpool July 24, 2020, 9:33pm 9

Thank you @tpoterba! I will try that.

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