Convert GWAS summary statistics to VCF

Tool to map GWAS summary statistics to VCF with on-the-fly harmonisation to a supplied reference FASTA

Produces GWAS-VCF with version 1.0 of the specification

Documentation

Full documentation available from https://mrcieu.github.io/gwas2vcf

GWAS summary statistics

Complete GWAS summary statistics in GWAS-VCF are available on >14,000 datasets from the OpenGWAS project

Tutorials

What can I do with GWAS-VCF?

• Command-line operations (filter, annotate, convert, liftover, merge, validate, pathway, gene)
• Integration with other tools (clumping, finemapping, LDSC, colocalization, Mendelian randomization, COJO)
• Parse (R, Python3)

Let us know if you have other use cases through the issues page!

Workflow

Citation

• Lyon M, Andrews S, Elsworth B, Gaunt T, Hemani G, Marcora E. The variant call format provides efficient and robust storage of GWAS summary statistics. Genome Biol 22, 32 (2021). https://doi.org/10.1186/s13059-020-02248-0

• Elsworth B, Lyon M, Alexander T, Liu Y, Matthews P, Hallett J, Bates P, Palmer T, Haberland V, Davey Smith G, Zheng J, Haycock P, Gaunt TR, Hemani G. The MRC IEU OpenGWAS data infrastructure. bioRxiv, p. 2020.08.10.244293, Aug. 2020. https://doi.org/10.1101/2020.08.10.244293

Please also cite the relevant tool(s) and data source if you use GWAS-VCF for downstream analyses.