BGT: efficient and flexible genotype query across many samples

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Abstract

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:hengli@broadinstitute.org

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