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Nat Methods. 2015 Nov;12(11):1061-3. doi: 10.1038/nmeth.3582. Epub 2015 Sep 14.

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

Author information

1
Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.
2
Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA.
3
Department of Genetics, Stanford University, Stanford, California, USA.
4
Department of Biology, Stanford University, Stanford, California, USA.
5
Howard Hughes Medical Institute, Stanford University, Stanford, California, USA.

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.

PMID:
26366987
PMCID:
PMC4626402
DOI:
10.1038/nmeth.3582
[Indexed for MEDLINE]
Free PMC Article

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