WASP: allele-specific software for robust molecular quantitative trait locus discovery
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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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WASP calibration was performed on raw BAM files to eliminate allelic bias towards reference alleles during alignment.
“To further eliminate allelic bias towards reference alleles during the alignment step, we performed WASP (v.0.3.4) calibration on the generated raw BAM files68.”
From PICALM Alzheimer’s risk allele causes aberrant lipid droplets in microglia (2025) · cites this paper as [68]
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“To further eliminate allelic bias towards reference alleles during the alignment step, we performed WASP (v.0.3.4) calibration on the generated raw BAM files 68 .”
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- Authors
- van de Geijn, B., McVicker, G., Gilad, Y., & Pritchard, J. K.
- Affiliations
- Stanford University (US)
- University of Chicago (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Pritchard, Jonathan K
- Venue
- Nature Methods
- Published
- 2015-09-14
- Volume
- 12
- Issue
- 11
- Pages
- 1061-1063
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC4626402
- OpenAlex
- W2221356560
- Cited by
- 575
- References
- 4
- Citations by year
- 2026: 42 · 2025: 70 · 2024: 75 · 2023: 70 · 2022: 48 · 2021: 70 · 2020: 53 · 2019: 56 · 2018: 29 · 2017: 30 · 2016: 27 · 2015: 5
- FWCI
- 13.32
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nd
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Science Foundation (0638477)
- Howard Hughes Medical Institute
- National Institutes of Health (MH101825)
- National Institute of Mental Health (MH101825, R01MH101825)
- National Human Genome Research Institute (R01HG006123, HG006123, HG007036, U01HG007036)
- National Institute of General Medical Sciences (GM007197, T32GM007197)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- RNA-seq, ChIP-seq, technical artifacts, open-source bioinformatics software, simulated reads
- MeSH terms
- Alleles, Genotype, Haplotypes, Heterozygote, Humans, Software, Reproducibility of Results, Likelihood Functions, Artifacts, Genome, Sequence Analysis, DNA, Sequence Analysis, RNA, Computational Biology, Quantitative Trait Loci, Chromatin Immunoprecipitation
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