If not stated otherwise, our tool was always used with the following settings. We extended gene regions by 50kb upstream and downstream for gene scoring. Only SNPs that reached a MAF of 0.05 in European 1KG sample were used. For pathway score calculation, we removed the HLA-region. The gene-fusion parameter was set to 1Mb, so that when calculating a particular pathway score, all pathway-member genes less than 1Mb apart were fused for the calculation. We also removed genes containing more than 3000 SNPs except during speed benchmarking (Fig 2) where all SNPs were used.
