Tutorials¶
To take Hail for a test drive, go through our tutorials. These can be viewed here in the documentation, but we recommend instead that you run them yourself with Jupyter.
Download the Hail distribution from our getting started page, and follow
the instructions there to set up the Hail. Inside the unzipped distribution folder, you’ll find
a tutorials/ directory. cd to this directory and run jhail to start the notebook
server, then click a notebook to begin!
Hail Overview¶
This notebook is designed to provide a broad overview of Hail’s functionality, with emphasis on the functionality to manipulate and query a genetic dataset. We walk through a genome-wide SNP association test, and demonstrate the need to control for confounding caused by population stratification.
Introduction to the expression language¶
This notebook starts with the basics of the Hail expression language, and builds up practical experience with the type system, syntax, and functionality. By the end of this notebook, we hope that you will be comfortable enough to start using the expression language to slice, dice, filter, and query genetic data.
Expression language: query, annotate, and aggregate¶
This notebook uses the Hail expression language to query, filter, and annotate the same thousand genomes dataset from the overview. We also cover how to compute aggregate statistics from a dataset using the expression language.
- Using the expression language to slice, dice, and query genetic data
- Check for tutorial data or download if necessary
- Types in action
- Filtering with expressions
- Filtering variants and genotypes
- Annotating with expressions
- Aggregables
- Count
- Sum
- Fraction
- Stats
- Counter
- FlatMap
- Take
- Collect
- takeBy
- Aggregating by key