GWIS - model-free, fast and exhaustive search for epistatic interactions in case-control GWAS

BMC Genomics

Table 1 Runtime required for GWIS compared to recent CPU and GPU methods.

Runtime required for GWIS compared to recent CPU and GPU methods. The first column reports results for WTCCC-sized data (450K SNPs, 5K samples) while the second column shows timings for larger recent GWAS (5M SNPs, 10K samples). The rightmost column denotes whether a method performs exhaustive search of all pairs. Filters run by GWIS are $χ^{2}$ alone or in combination with DSS and SS tests. The times indicated by '*' are actual run times, and all other times are estimated by scaling (see Supplement Section 2 for exact calculations). Runtime for non-exhaustive methods has not been estimated as it is difficult to judge how these methods scale with the number of SNPs and samples.

ISSN: 1471-2164