There is a robust implementation of HWE Test that takes into account population substructure: RUTH - Robust Unified Hardy-Weinberg Equilibrium Test. It is used for the TopMed pipeline. The GitHub repository is here: [image] statgen/ruth Robust Unified Hardy-Weinberg Equilibrium Test. C…

Has there been any progress on implementing a version of RUTH in hail?

We’re still building out the ndarray infrastructure that will let us write hl.logistic_regression_rows in Python. I’m not sure exactly the timeline, but I’d hope we have the set of features necessary to implement RUTH in Hail in Python done by the end of 2020.

Hail implementation of RUTH

Feature Requests

tpoterba October 8, 2019, 6:12pm 2

it looks like all we need is a way to do logistic regression on an arbitrary array/ndarray. Thanks for the submission, this should be feasible to implement in not too long, I think.

Topic		Replies	Views
PheWAS on DNAnexus UKB RAP Hail Query & hailctl	13	918	December 21, 2022
Filtering samples with extreme heterozygosity in hail? Hail Query & hailctl	7	1270	February 19, 2020
Added ability to compute HWE on subsets of samples Updates	0	997	November 7, 2016
Big picture issues: considering switching to HAIL Meta	6	4007	January 3, 2023
GWAS on subset of UKBioBank Hail Query & hailctl	26	1686	July 13, 2021

Hail implementation of RUTH

Related topics