hours which is ∼16 times faster than running the same number of permutations with Matrix eQTL (Table 1). When using only 100 permutations, this is reduced to only ∼33 CPU hours. Table 1.FastQTL and Matrix eQTL running timesNumber of permutationsMatrix eQTLFastQTL10001000500100GTEx_AS337.41910.83.5GTEx_AT330.32110.83.6GTEx_HLV312.41583GTEx_L364.925.613.14GTEx_MS335.923.612.63.9GTEx_NT343.818.49.53.4GTEx_SSEL349.720.710.83.6GTEx_T358.122.311.83.9GTEx_WB340.525.513.74.1ALL3073191.1101.133Table 1 shows the running times in CPU hours to produce the results shown in Figure 2e; nine GTEx datasets (column 1) processed with 1000 Matrix eQTL permutations (column 2) and FastQTL with 1000 (column 3), 500 (column 4) and 100 permutations (column 5). Total running times for all nine datasets together are shown in the last row.
