Genetic variation in cis-regulatory elements is an important cause of variation in gene expression. Cis-regulatory variation can be detected by using high-throughput RNA sequencing (RNA-seq) to identify differences in the expression of the two alleles of a gene. This requires that reads from the two alleles are equally likely to map to a reference genome(s), and that single-nucleotide polymorphisms (SNPs) are accurately called, so that reads derived from the different alleles can be identified. Both of these prerequisites can be achieved by sequencing the genomes of the parents of the individual being studied, but this is often prohibitively costly.