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 .

Hi Liverpool! Thank you for your interest in Hail! Yes, you should be able to import HDFS files into Hail which will then be formatted into a Hail matrix table for ease in computation https://hail.is/docs/0.2/utils/index.html#hail.utils.hadoop_open As for a linear regression of genotype or allele…

Kumar, they are not talking about “HDFS”. It’s a 5, not an S.

After talking to John offline, I made an error and you would have to attempt to read the HDF5 file into a format that we will be able to import the file into the Hail environment e.g. a vcf file.

An HDF5 file importer is something we should add in the future, but unfortunately we haven’t yet.

Thanks for your reply! I could use h5py package to read the hdf5 file into python, and extract the genotype data as a numpy matrix, so could I somehow convert it to Hail matrix table or other format that Hail could understand?

Read HDF5 file and run GWAS

Hail Query & hailctl

Liverpool July 24, 2020, 9:33pm 9

Thank you @tpoterba! I will try that.

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Read HDF5 file and run GWAS

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