We improved the efficiency of GENIE-mem in this version. GENIE-v1.1 has the following major changes:
- In the first pass, the code reads SNPs in blocks according to a new parameter (mem_Nsnp), which is turned on by the parameter opt1 (opt1=1). This parameter can be set independently of the number of jackknife blocks.
- To speed up computation, GENIE writes the jackknife block-level statistics from pass 1 to file and is turned on by the parameter opt2 (opt2=1). These statistics are read in pass 2 (instead of recomputing them from the genotypes as in the previous version).
- These two optimizations are turned on as the default. Setting opt1=opt2=0 will revert to the previous version of GENIE.
- The statistics output at the end of pass one only depends on genotypes (and covariates, annotations). GENIE-v1.1 can read these pre-computed statistics and combine them with a new phenotype (summary_genotype=<filename prefix>).