hail 0.2.15

Scalable library for exploring and analyzing genomic data.

Hail

Hail is an open-source, general-purpose, Python-based data analysis tool with additional data types and methods for working with genomic data.

Hail is built to scale and has first-class support for multi-dimensional structured data, like the genomic data in a genome-wide association study (GWAS).

Hail is exposed as a Python library, using primitives for distributed queries and linear algebra implemented in Scala, Spark, and increasingly C++.

See the documentation for more info on using Hail.

Contribute

If you'd like to discuss or contribute to the development of methods or infrastructure, please:

• see the For Software Developers section of the installation guide for info on compiling Hail
• chat with us about development in our Zulip chatroom
• visit the Development Forum for longer-form discussions

Hail uses a continuous deployment approach to software development, which means we frequently add new features. We update users about changes to Hail via the Discussion Forum. We recommend creating an account on the Discussion Forum so that you can subscribe to these updates as well.

Maintainer

Hail is maintained by a team in the Neale lab at the Stanley Center for Psychiatric Research of the Broad Institute of MIT and Harvard and the Analytic and Translational Genetics Unit of Massachusetts General Hospital.

Contact the Hail team at [e-mail].

Citing Hail

If you use Hail for published work, please cite the software. You can get a citation for the version of hail you installed by executing:

import hail as hl

print(hl.cite_hail())

Which will look like:

Hail Team. Hail 0.2.13-81ab564db2b4. https://github.com/hail-is/hail/releases/tag/0.2.13.

Or if you need a bibtex entry:

import hail as hl

print(hl.cite_hail_bibtex())

Which will look like:

@misc{Hail,
  author = {Hail Team},
  title = {Hail},
  howpublished = {\url{https://github.com/hail-is/hail/releases/tag/0.2.13}}
}

If you simply cannot stomach the idea of citing a GitHub repository (even though more than 2,800 people have cited the Keras GitHub repository), then please cite this DOI which always points to the latest published version of Hail:

Hail Team. Hail. http://doi.org/10.5281/zenodo.2646680

Acknowledgements

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.