Reduction of the cost of genotyping by reducing the number of sequences in a multiplex having repetitive elements. The cost of genotyping using SNPstream 48-plex assays was calculated for a 100% pass rate (1 on y-axis): this cost increases non-linearly, as the pass rate decreases. Here we show how the cost increases with the number of assays containing repetitive sequences, per multiplex. Some repetitive sequences clearly affect the pass rate in the whole multiplex. We now use Seq4SNPs with Repeat Masker output, put masked sequences output from Seq4SNPs into SNP-IT primer design software for SNPstream, and replace SNPs rejected by SNP-IT. This improves assay success and reduces the cost of genotyping significantly.