Deal with phased genotyping data

TARGENE / targene-pipeline

Nextflow pipeline for Targeted-Learning of genetic effects

MIT License

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Deal with phased genotyping data #52

Open olivierlabayle opened 1 year ago

olivierlabayle commented 1 year ago

Support is provided only for unphased genotypes at the moment.

This causes (undetectable) issues in the tests at the moment.

olivierlabayle commented 1 year ago

Support for phased data may be actually quite complex and not immedialtely of interest then:

[x] convert test data to unphased data
[ ] add a check at the variant level that it is actually unphased otherwise undesired behaviour will silently occur --> this may be solved by https://github.com/OpenMendel/BGEN.jl/issues/29

kose-y commented 1 year ago

Currently, the first_allele_dosage!() function in the BGEN package supports unphased data through the first_dosage_phased!() function (https://github.com/OpenMendel/BGEN.jl/blob/main/src/genotypes.jl#L366), and if some undesired behavior is happening, it might a bug in that function.