Extended Data Fig. 7: Allele-specific expression benchmark using RNA-seq data from NA12878.

Allele-specific expression (ASE) results comparing the MPMAP-RPVG pipeline against WASP (with STAR as the aligner) using simulated data. Shows true positive rate and false positive rate of ASE significance for different thresholds of variant read count in the simulated data. Variants were defined as showing significant ASE using a two-sided binomial test of the allele-specific read counts with p-values adjusted using the Benjamini-Hochberg procedure and a False Discovery Rate (FDR) α = 0.1. All heterozygotic NA12878 variants from the 1000 Genomes Project (1000GP) with at least one read in the simulated data were used for the benchmark. For the MPMAP-RPVG pipeline, we used the personal transcriptome generated from the 1000GP NA12878 haplotypes (Supplementary Table 3). WASP was provided the 1000GP NA12878 haplotypes as input. Note, we only used WASP for bias correction and allele-specific read counting, and not its downstream inference method.