vamos

vamos annotates variable-number tandem repeats (VNTRs) by using efficient motif sets and repeat-composition-based annotation across motif diversity levels to improve characterization and allele estimation of VNTR variability in genomic sequences.

Key Features:

• VNTR scope: Targets VNTR loci composed of motifs of at least six bases that comprise approximately 3% of the human genome and are highly polymorphic.
• Efficient motif sets: Represents repeat diversity using efficient motif sets to reduce redundancy in VNTR annotation.
• Composition-based annotation: Annotates VNTRs based on repeat composition rather than alignment breakpoints.
• Motif diversity levels: Performs annotation under varying levels of motif diversity to capture nuanced repeat variation.
• Comparative allele estimation: Reports allele counts of 7.4–16.7 per locus across 74 haplotype-resolved human assemblies versus 4.0–5.5 alleles per locus from breakpoint-based approaches.
• Assembly compatibility: Applied to haplotype-resolved human assemblies for allele discovery and locus-level analysis.

Scientific Applications:

• VNTR characterization: Characterizing VNTR sequence composition and allele diversity in genomic studies.
• Population genetics: Analyzing VNTR variation for population-genetic investigations.
• Disease association studies: Supporting disease-association analyses that require precise VNTR genotyping.
• Genetic linkage: Informing genetic linkage analyses through improved VNTR allele definitions.

Methodology:

Annotates VNTRs by analyzing repeat composition under varying motif diversity levels, leverages efficient motif sets to represent repeat diversity, and compares composition-based annotations to alignment breakpoint–based variant definitions; applied to 74 haplotype-resolved human assemblies to estimate alleles per locus.