Brief Communication | Published:

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

Nature Methods volume 12, pages 10611063 (2015) | Download Citation

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.

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Acknowledgements

We thank members of the Liu, Pritchard, Stephens and Gilad labs for helpful discussions. We thank X.S. Liu's lab for hosting G.M. as a visitor in the Department of Biostatistics and Computational Biology at the Dana-Farber Cancer Institute while this work was conducted. We thank many early users of WASP, particularly C. DeBoever, who contributed bug fixes and code improvements. This work was supported by the Howard Hughes Medical Institute, the US National Institutes of Health (NIH grants HG007036, HG006123, MH101825 and GM007197) and the US National Science Foundation (NSF Graduate Research Fellowship DGE-0638477 to B.v.d.G.).

Author information

Author notes

    • Bryce van de Geijn
    •  & Graham McVicker

    These authors contributed equally to this work.

Affiliations

  1. Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.

    • Bryce van de Geijn
    •  & Yoav Gilad
  2. Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA.

    • Bryce van de Geijn
  3. Department of Genetics, Stanford University, Stanford, California, USA.

    • Graham McVicker
    •  & Jonathan K Pritchard
  4. Department of Biology, Stanford University, Stanford, California, USA.

    • Jonathan K Pritchard
  5. Howard Hughes Medical Institute, Stanford University, Stanford, California, USA.

    • Jonathan K Pritchard

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Contributions

B.v.d.G., G.M., J.K.P. and Y.G. conceived of the project. B.v.d.G. and G.M. performed the analyses and implemented the software. G.M. and B.v.d.G. wrote the manuscript with input from all authors. J.K.P. and Y.G. directed the project.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Jonathan K Pritchard.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–5, Supplementary Table 1 and Supplementary Notes 1–8

Zip files

  1. 1.

    Supplementary Software

    WASP code and documentation. Updated files are maintained at https://github.com/bmvdgeijn/WASP

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DOI

https://doi.org/10.1038/nmeth.3582

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