In addition to prioritizing on the basis of a SNPs' position and effect on a gene, Tabor et al. (1) further suggested filtering high-priority SNPs based on their allele frequencies, and using haplotype information to select a single SNP for genotyping if several SNPs are known to be in linkage disequilibrium. Though FASTSNP does not currently integrate this type of information in the prioritization method, it does provide their haplotype information in the output function report.
