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projectglow / glow

An open-source toolkit for large-scale genomic analysis
https://projectglow.io
Apache License 2.0
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Interaction Tests with GLOW #530

Open jjfarrell opened 1 year ago

jjfarrell commented 1 year ago

Can GLOW run interaction tests for a gwas analyses? Regenie presently can perform interaction tests (GxE, GxG). If that is not yet available in GLOW, could that be ported to GLOW?

williambrandler commented 1 year ago

@jjfarrell it could be possible to do this with the Glow Pipe Transformer

for example if you joined the variants to the --interaction-snp-file, partitioned on the set of interacting SNPs you want to test and then fed the resulting dataframe through the pipe transformer, running regenie on the command line for each partition

@henrydavidge what do you think?