VADT

VADT detects allele-specific expression (ASE) from RNA-seq-derived single nucleotide polymorphisms (SNPs) by processing Variant Call Format (VCF) files and applying statistical tests to reveal cis-regulatory allelic imbalance in diploid organisms.

Key Features:

• VCF File Processing: Performs filtering on VCF files including exclusion of variants failing the FILTER column and retention of variants marked "PASS".
• RNA-seq-derived SNP handling: Operates on SNPs derived from RNA-seq data for ASE analysis in diploid organisms.
• Customizable Filtering Criteria: Allows user-defined exclusion of variants within a specified distance from indels, removal of multiallelic variants to retain biallelic SNPs, and application of a user-defined minimum quality score threshold.
• ASE Detection Methodology: Tests biallelic SNPs for allele-specific expression using a binomial test.

Scientific Applications:

• ASE analysis in broiler chicken tissues: Applied to breast muscle, abdominal fat, and liver from commercial broiler chickens (n = 68), with ~174,000 SNPs per tissue passing filters and ~24,000 SNPs (~14%) exhibiting ASE.
• Tissue-specific ASE detection: Identified that ~83% of ASE SNPs were specific to a single tissue and 3.7% of ASE SNPs were expressed across all three tissues.
• Comparative ASE gene overlap and pathway enrichment: Reported ASE gene overlap among all three tissues at 20.1% and enrichment of ASE genes in pathways including translation.

Methodology:

Processes VCFs of RNA-seq-derived SNPs by retaining variants with FILTER="PASS", excluding variants within a user-defined distance from indels, removing multiallelic variants, applying a user-defined minimum quality score, and testing biallelic SNPs for ASE using a binomial test.