Fig. 1.

Performance comparison for querying summary statistics in plain text and GWAS-VCF. Mean query time (seconds, lower is quicker; repetitions n = 100) to extract either a single variant using the chromosome position or dbSNP [31] identifier or multiple variants using a 1-Mb interval or association P value. AWK, grep, bcftools [23] and rsidx [32] were evaluated using uncompressed/GZIP compressed TSV and BGZIP [23] compressed VCF. The summary statistics files contained one (single) or five (multiple) GWAS studies which were prepared by subsampling variants (n = 0.5 M, 2.5 M, 10 M) obtain from Neale et al. [35]. Error bars represent the 95% confidence interval