Work

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

Year: 2020

Type: article

Abstract: SUMMARY: 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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btaa628

Authors: Lina Yang, Shuang Jiang, Bibo Jiang, Dajiang J Liu, Xiaowei Zhan

Institutions: Pennsylvania State University, The University of Texas Southwestern Medical Center

Language: English

Topic: Genetic Associations and Epidemiology

Subfield: Genetics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: bronze

Funders: National Institutes of Health, National Human Genome Research Institute, National Institute of General Medical Sciences

Awards: Method to Enhance the Rare Variant Genetic Architecture Analysis in Meta-Analyses, Tools for integrative genomics and disease association study for the X chromosome, Methods to Identify, Validate & Interpret GWAS Loci in Multi-ethnic Meta-analysis