QuASAR

QuASAR: Joint Genotype and Allele-Specific Expression Inference

QuASAR implements a statistical framework for joint genotyping from next-generation sequencing data and allele-specific expression (ASE) inference, enabling analysis of heterozygous sites directly from RNA-seq reads in expression quantitative trait loci (eQTL) studies.

Key Features:

• Joint Inference of Genotypes and ASE: Simultaneously infers genotypes and tests for allelic imbalance at heterozygous loci using RNA-seq data.
• Genotype Uncertainty Modeling: Incorporates uncertainty in genotype calls during ASE inference by modeling base-call errors and allelic over-dispersion.
• Robustness to Sequencing Depth: Maintains performance across varying sequencing depths and replicate datasets.

Scientific Applications:

• eQTL Analysis: Detects heterozygous variants and quantifies their effects on gene expression through ASE to identify regulatory genetic variants.
• Regulatory Variant Characterization: Evaluates functional effects of non-coding sequence variation on gene regulation.

Methodology:

Applies a probabilistic model to next-generation RNA-seq reads to jointly estimate genotype probabilities and allelic expression ratios at candidate loci, explicitly accounting for base-calling errors and over-dispersion in allelic counts to improve statistical inference of allele-specific expression.