To perform a comprehensive evaluation of FastQTL, we used RNA-seq and genotype data produced by both the Geuvadis (Lappalainen et al., 2013; Supplementary material 1) and the GTEx consortia (GTEx Consortium, 2015; Supplementary material 2), two of the largest eQTL studies performed to date. This comprises a total of 10 distinct datasets with between 14 and 35K quantified genes and 6.8–10.8M variant sites for 83–373 samples (Supplementary Table 1).
