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The variant call format provides efficient and robust storage of GWAS summary statistics.

TitleThe variant call format provides efficient and robust storage of GWAS summary statistics.
Publication TypeJournal Article
Year of Publication2021
AuthorsLyon MS, Andrews SJ, Elsworth B, Gaunt TR, Hemani G, Marcora E
JournalGenome Biol
Volume22
Issue1
Pagination32
Date Published2021 01 13
ISSN1474-760X
KeywordsDatabases, Genetic, Genome-Wide Association Study, Genomics, Humans, Software
Abstract

GWAS summary statistics are fundamental for a variety of research applications yet no common storage format has been widely adopted. Existing tabular formats ambiguously or incompletely store information about genetic variants and associations, lack essential metadata and are typically not indexed yielding poor query performance and increasing the possibility of errors in data interpretation and post-GWAS analyses. To address these issues, we adapted the variant call format to store GWAS summary statistics (GWAS-VCF) and developed open-source tools to use this format in downstream analyses. We provide open access to over 10,000 complete GWAS summary datasets converted to this format ( https://gwas.mrcieu.ac.uk ).

DOI10.1186/s13059-020-02248-0
Pubmed Linkhttps://www.ncbi.nlm.nih.gov/pubmed/33441155?dopt=Abstract
page_expoInternal
Alternate JournalGenome Biol
PubMed ID33441155
PubMed Central IDPMC7805039
Grant List / DH_ / Department of Health / United Kingdom
208806/Z/17/Z / WT_ / Wellcome Trust / United Kingdom
U01 AG052411 / AG / NIA NIH HHS / United States
K99 AG070109 / AG / NIA NIH HHS / United States
MC_UU_00011/4 / MRC_ / Medical Research Council / United Kingdom
U01 AG058635 / AG / NIA NIH HHS / United States

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