Table 1 Summary of cost and runtime for association analysis pipeline using RAPpoet. Note that the cost and runtime of each step is a function of EC2 instance type, job priority, etc. See supplementary material and tables for more detailed costings and runtime. Note that fine mapping was run locally as PolyFun was not available on the UKB RAP.
Step | Chromosome 9 | Chromosome 21 | ||
|---|---|---|---|---|
Cost (£) | Runtime (Min) | Cost (£) | Runtime (Min) | |
Quality Control Step One | 176.50 | 1103 | 97.05 | 323 |
Quality Control Step Two | 33.33 | 855 | 5.41 | 216 |
sLR | 0.078 | 15 | 0.033 | 6 |
REGENIE | 2.75 | 91 | 0.23 | 31 |
VariantSpark | 179.31 | 796 | 56.14 | 499 |