Seqminer2: An efficient tool to query and retrieve genotypes for statistical genetics analyses from biobank scale sequence dataset

Lina Yang, Shuang Jiang, Bibo Jiang, Dajiang J. Liu, Xiaowei Zhan

Research output: Contribution to journalArticlepeer-review

Abstract

Here, we present a highly efficient R-package seqminer2 for querying and retrieving sequence variants from biobank scale datasets of millions of individuals and hundreds of millions of genetic variants. Seqminer2 implements a novel variant-based index for querying VCF/BCF files. It improves the speed of query and retrieval by several magnitudes compared to the state-of-the-art tools based upon tabix. It also reimplements support for BGEN and PLINK format, which improves speed over alternative implementations. The improved efficiency and comprehensive support for popular file formats will facilitate method development, software prototyping and data analysis of biobank scale sequence datasets in R. Availability and implementation: The seqminer2 R package is available from https://github.com/zhanxw/seqminer. Scripts used for the benchmarks are available in https://github.com/yang-lina/seqminer/blob/master/seqminer2%20benchmark%20script.txt.

Original languageEnglish (US)
Pages (from-to)4951-4954
Number of pages4
JournalBioinformatics
Volume36
Issue number19
DOIs
StatePublished - Oct 1 2020

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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