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

By Bryce van de Geijn, Graham P. McVicker, Yoav Gilad, J. K. Pritchard. Nature Methods, 2015

530 citations recorded by the source corpus.

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.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2a841f52ce3f47dc194752464d9ec4e28145e7b9

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Citations in the corpus

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells (2016, unknown): “…hypothesis correction (LRVM) Battle et al., 2014 http://dags.stanford.edu/dgn/ heritability analysis (GCTA) Yang et al., 2011 http://cnsgenomics.com/software/gcta/ Pysam N/A https://github.com/pysam-developers/pysam WASP van de Geijn et al., 2015 https://github.com/bmvdgeijn/WASP qvalue (v1.”
Impacts of Neanderthal-introgressed sequences on the landscape of human gene expression (2017, unknown): “…methods have been developed to detect allele-specific expression (ASE) in a single sample (Skelly et al., 2009), across individuals (van de Geijn et al., 2015), or across tissues (Pirinen et al., 2015), no generalized approach has been developed to combine all information simultaneously.”
Reference-based phasing using the Haplotype Reference Consortium panel (2016, methodology): “In particular, methods for mapping molecular QTLs using allele-speciﬁc reads require accurate phasing information, but recent papers introducing these methods have reported that inaccurate phasing currently limits their potential [16, 17].”