Moving to denser SNP maps, however, comes at the expense of increasing computational time. We performed analyses in SOLAR using the RAM drive rather than the hard drive, which decreased the computation time by ~50%. Each analysis of the simulated chromosome 1 data took approximately 23 minutes for the microsatellite map (38 markers), 3–5 hours for the SNP1 map (381 markers), and 15–19 hours for the SNP2 map (864 markers). At the time of our analysis, SOLAR was unable to handle more than 500 markers per chromosome, so we had to break the SNP2 data into two to three sections for the larger chromosomes. This complicated the analysis as we had to "bridge" across sections to minimize boundary effects when estimating multipoint IBDs. The latest release of SOLAR 2.1.4 can handle up to 2000 markers, but the computation time may still be quite substantial.
