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arXiv:1506.08452q-bio.GN

BGT: efficient and flexible genotype query across many samples

Heng Li

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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 7.4GB database and decodes a couple of hundred 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

arXiv comments
Identical to the published version except formatting
Journal reference
Bioinformatics, 32: 590-2 (2016)
DOI
doi:10.1093/bioinformatics/btv613
Subjects
q-bio.GNGenomics

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  1. Big Data: Astronomical or Genomical? 1 comment

    • Better representations are already used for downstream data analysis and continue to be improved; see e.g. http://arxiv.org/abs/1506.08452 . However, algorithms for producing variant calls from raw sequencer output are also improving over time, and the way to get the most…

      temujinView on HNParent context

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