https://github.com/vjcitn/biochail

Using hail via Basilisk
https://github.com/vjcitn/biochail

bioconductor genetics hail r

Last synced: about 1 month ago
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Using hail via Basilisk

• Host: GitHub
• URL: https://github.com/vjcitn/biochail
• Owner: vjcitn
• License: gpl-3.0
• Created: 2022-12-10T14:20:06.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2023-06-05T01:11:07.000Z (almost 2 years ago)
• Last Synced: 2024-10-28T12:40:44.943Z (7 months ago)
• Topics: bioconductor, genetics, hail, r
• Language: R
• Homepage: https://vjcitn.github.io/BiocHail
• Size: 18 MB
• Stars: 6
• Watchers: 4
• Forks: 0
• Open Issues: 4
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

        
# BiocHail

This is a multi-step overview of Hail for genetic association

studies

## Tutorial overview

The basic layout, following the [Hail GWAS tutorial](https://hail.is/docs/0.2/tutorials/01-genome-wide-association-study.html):

![topics](https://github.com/vjcitn/BiocHail/raw/main/toc1.png)

We'll see how to use a very small excerpt from the

1000 genomes study to produce

![litman](https://github.com/vjcitn/BiocHail/raw/main/litman.png)

Along the way, we illustrate and adjust for population stratification:

![popstrat](https://github.com/vjcitn/BiocHail/raw/main/popstrat.png)

## Larger data problem -- 1000 genomes data with T2T reference

We have arranged a serialization of genotypes on chromosome 17

for 3202 1000 genomes samples.

## Relevant LD resources ... in which cloud?

Still to come.

## Simulating multipopulation genotype surveys

Still to come.

## Binding phenotypes from FHIR to Hail

Still to come.