Summary: BGT is a compact format, a fast command line tool and a simple web application for efficient and convenient query of whole-genome genotypes and frequencies across tens to hundreds of thousands of samples. On real data, it encodes the haplotypes of 32 488 samples across 39.2 million SNPs into a 7.4 GB database and decodes up to 420 million genotypes per CPU second. The high performance enables real-time responses to complex queries.

Availability and implementation:  https://github.com/lh3/bgt

Contact:  [email protected]

© The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: [email protected]
2015