3.2 of Shabalin, 2012). Then, two multiple-testing levels are accounted for to determine the whole-genome significance of this nominal P-value and thereby to consider the corresponding variant q as a QTL: multiple genetic variants are tested per phenotype and multiple phenotypes are tested genome-wide. Following common usage, FastQTL uses permutations to correct for the former (see Sections 2.3–2.5) and FDR estimation to control for the latter (see Section 2.6).
