Powering genomic analysis, at every scale

An open-source library for scalable genomic data exploration
GWAS with Hail (click to show code)

Install

pip install hail

Hail requires Python 3 and the Java 8 JRE

GNU/Linux wil also need C and C++ standard libraries if not already installed

Detailed instructions

Features

Simplified Analysis

Hail is an open-source Python library that simplifies genomic data analysis. It provides powerful, easy-to-use data science tools that can be used to interrogate even biobank-scale genomic data (e.g UK Biobank, TopMed, FinnGen, and Biobank Japan).

Genomic Dataframes

Modern data science is driven by table-like data structures, often called dataframes (see Pandas). While convenient, they don't capture the structure of genetic data, which has row (variant) and column (genotype) groups. To remedy this, Hail introduces a distributed, dataframe-like structure called MatrixTable.

Input Unification

The Hail MatrixTable unifies a wide range of input formats (e.g. vcf, bgen, plink, tsv, gtf, bed files), and supports scalable queries, even on petabyte-size datasets. By leveraging MatrixTable, Hail provides an integrated, scalable analysis platform for science.

Learn More >

Acknowledgments

The Hail team has several sources of funding at the Broad Institute:

  • The Stanley Center for Psychiatric Research, which together with Neale Lab has provided an incredibly supportive and stimulating home.
  • Principal Investigators Benjamin Neale and Daniel MacArthur, whose scientific leadership has been essential for solving the right problems.
  • Jeremy Wertheimer, whose strategic advice and generous philanthropy have been essential for growing the impact of Hail.

We are grateful for generous support from:

  • The National Institute of Diabetes and Digestive and Kidney Diseases
  • The National Institute of Mental Health
  • The National Human Genome Research Institute
  • The Chan Zuckerburg Initiative

We would like to thank Zulip for supporting open-source by providing free hosting, and YourKit, LLC for generously providing free licenses for YourKit Java Profiler for open-source development.