title: WASP: allele-specific software for robust molecular quantitative trait locus discovery.
abstract: 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.
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.|Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA.
authors.forename: Bryce
authors.initials: B
authors.lastname: van de Geijn
authors.affiliation: Department of Genetics, Stanford University, Stanford, California, USA.
authors.forename: Graham
authors.initials: G
authors.lastname: McVicker
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.
authors.forename: Yoav
authors.initials: Y
authors.lastname: Gilad
authors.affiliation: Department of Genetics, Stanford University, Stanford, California, USA.|Department of Biology, Stanford University, Stanford, California, USA.|Howard Hughes Medical Institute, Stanford University, Stanford, California, USA.
authors.forename: Jonathan K
authors.initials: JK
authors.lastname: Pritchard
mesh_terms: D000483:Alleles; D016477:Artifacts; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods*; D016678:Genome; D005838:Genotype; D006239:Haplotypes; D006579:Heterozygote; D006801:Humans; D016013:Likelihood Functions; D040641:Quantitative Trait Loci; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software