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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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Quickstart #431

Closed williambrandler closed 2 years ago

williambrandler commented 3 years ago

What changes are proposed in this pull request?

Quickstart guide for running GWAS

Designed to get people up and running quickly with glow. Uses simulated data from https://github.com/projectglow/glow/pull/427

Replaces the old gwas demo.

To make this demo work, changed the notebooks tests to run sequentially rather than in parallel. This takes longer but will allow for an end-to-end integration test of all the notebooks, where notebooks depend on the output of the other notebooks.

Includes variant and sample quality control, whole genome regression,

And a demo of the fix for missingness that causes confounding, which was resolved partially by https://github.com/projectglow/glow/pull/416

How is this patch tested?

(Details)

codecov[bot] commented 3 years ago

Codecov Report

Merging #431 (f0f3f5f) into master (d03b415) will not change coverage. The diff coverage is n/a.

Impacted file tree graph

@@           Coverage Diff           @@
##           master     #431   +/-   ##
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  Coverage   93.63%   93.63%           
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  Files          95       95           
  Lines        4824     4824           
  Branches      466      466           
=======================================
  Hits         4517     4517           
  Misses        307      307

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