| Model for the soft elastic substrate | In order to save computation time , but still keep a high local resolution, local mesh refinement is applied to the top surface. |
| Optimization | As this is expensive in terms of computation time , the numerical work is parallelized using the boost thread library [50]. |
| Optimization | The computation time on 8 cores of current Intel i7 processors is on the order of 15 minutes per iteration step. |
| Cross Validation | We then masked the framework genotypes of the 1,317 individuals whose genomes were not sequenced, imputed the framework genotypes, and calculated the concordance between the imputed and true genotypes over a sample of 53,861 framework SNVs (sorted by base-pair position, every 5th framework SNV was picked instead of using all SNVs to save computing time ). |
| Discussion | PRIMAL can be applied to other founder populations or to large families to provide accurate and nearly complete genotype coverage for relatively very small cost and minimal computation time . |
| Pedigree-based Imputation | Finding and indexing IBD segments into cliques takes the majority of computing time in the PRIMAL pipeline. |