FastMap is a software for fast and efficient eQTL mapping in homozygous inbred populations with binary allele calls. FastMap exploits the discrete nature and structure of the measured single nucleotide polymorphisms (SNPs). In particular, SNPs are organized into a Hamming distance-based tree that minimizes the number of arithmetic operations required to calculate the association of a SNP by making use of the association of its parent SNP in the tree. FastMap’s tree can be used to perform both single marker mapping and haplotype association mapping over an m-SNP window. These performance enhancements also permit permutation-based significance testing.
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D.M. Gatti, A.A. Shabalin, T.C. Lam, F.A. Wright, I. Rusyn, and A.B. Nobel.
FastMap: Fast eQTL mapping in homozygous populations.
Bioinformatics, 25(4):482, 2009.