VAP

VAP detects genomic variants from transcriptome sequencing (RNA-seq) data to identify single nucleotide polymorphisms (SNPs) and RNA editing events within expressed genomic regions.

Key Features:

• Splice-Aware Alignment: VAP employs multiple RNA-seq splice-aware aligners for accurate mapping of reads in alternatively spliced transcriptomes.
• SNP Detection in Non-Human Models: VAP identifies SNPs using RNA-seq data alone and is specifically applicable to non-human model organisms.
• High Accuracy and Validation: In a validation study on a highly inbred chicken line, VAP recovered over 65% of coding variants that were also detected by whole-genome sequencing (WGS).
• Detection of Post-Transcriptional Modifications: VAP detects variants arising from post-transcriptional modifications, such as RNA editing, from RNA-seq data.
• Focus on Expressed Regions: VAP detects variants only within expressed regions, enabling targeted analysis of functionally relevant genetic variation.

Scientific Applications:

• Evolutionary Biology: Investigating genetic diversity and phenotypic variation across populations using expressed variants.
• Functional Genomics: Identifying coding variants and RNA editing events that may affect gene function and regulation.
• Comparative Transcriptomics: Comparing expressed variant landscapes across samples, strains, or species.
• Breeding and Conservation: Informing breeding programs and conservation efforts by detecting expressed SNPs linked to traits.
• Biomedical Research: Characterizing expressed genetic variation relevant to disease mechanisms and gene-expression studies.

Methodology:

VAP uses multiple RNA-seq splice-aware aligners and performs SNP detection from RNA-seq reads; validation included comparison to WGS in an inbred chicken line with >65% concordance for coding variants.