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
Full documentation available from https://mrcieu.github.io/gwas2vcf
Complete GWAS summary statistics in GWAS-VCF are available on >14,000 datasets from the OpenGWAS project
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!
-
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.