WASP: allele-specific software for robust molecular quantitative trait locus discovery.

van de Geijn B, McVicker G, Gilad Y, Pritchard JK.
Nature methods. 2015 Nov;12(11):1061-3.
Allele-specific sequencing reads provide a powerful signal for identifying molecular quantitative trait loci (QTLs), but they are challenging to analyze and are prone to technical artifacts. Here we describe WASP, a suite of tools for unbiased allele-specific read mapping and discovery of molecular QTLs. Using simulated reads, RNA-seq reads and chromatin immunoprecipitation sequencing (ChIP-seq) reads, we demonstrate that WASP has a low error rate and is far more powerful than existing QTL-mapping approaches.