mrcieu/gwas2vcf repository overview

⁠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!

⁠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.