The ALLELE Procedure

The WITH statement has the same syntax as the VAR statement. It contains variables of alleles, or genotypes if GENOCOL is specified, from markers that you want to pair with those specified in the VAR statement for linkage disequilibrium calculations. Each marker from the VAR statement is paired with each marker from the WITH statement for these two-marker statistics when the WITH statement is specified. The markers represented by variables in this statement are not included in any of the single-marker calculations (marker summary statistics, allele frequencies, or genotype frequencies) and the associated ODS tables. This statement facilitates the parallelization of the LD calculations.

When the WITH statement is used, the MAXDIST= option is ignored. It cannot be used for data in the tall format.