gwas2vcf: convert GWAS summary statistics to VCF

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

Produces GWAS-VCF with version 1.0 of the specification

Data

Full GWAS summary statistics harmonised to GWAS-VCF are available on >14,000 datasets available from https://gwas.mrcieu.ac.uk/

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