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Updated: Apr 26, 2026
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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
Published on: June 23, 2012
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VNTRseek-a computational tool to detect tandem repeat variants in high-throughput sequencing data
Yevgeniy Gelfand1, Yozen Hernandez2, Joshua Loving2
1Laboratory for Biocomputing and Informatics, Boston University, Boston, MA 02215, USA.
Nucleic Acids Research
|July 25, 2014
Summary
VNTRseek software discovers minisatellite variable number tandem repeats (VNTRs) using whole genome sequencing. This tool identifies VNTRs across diverse genomes, enabling new insights into genomic variation and inheritance patterns.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- DNA tandem repeats (TRs) are repetitive sequences in genomes.
- Variable number tandem repeats (VNTRs) are polymorphic TRs with varying copy numbers.
- Minisatellite VNTRs have pattern sizes of 7 nucleotides or more.
Purpose of the Study:
- To introduce VNTRseek, a novel software for detecting minisatellite VNTRs.
- To enable genome-wide discovery of VNTRs using whole genome sequencing data.
Main Methods:
- VNTRseek maps sequencing reads to reference TRs.
- It identifies VNTRs by comparing read copy numbers to reference copy numbers.
- The software was tested on Watson, Khoisan, and 1000 Genomes family trio genomes.
Main Results:
- VNTRseek identified 752 VNTRs in the Watson genome (7-84 nt patterns).
- It detected 2572 VNTRs in the Khoisan genome (7-105 nt patterns).
- In trios, 2660-3822 VNTRs per individual were found with high Mendelian inheritance consistency.
Conclusions:
- VNTRseek is the first software for genome-wide minisatellite VNTR detection.
- The software facilitates the study of VNTRs in various genomic contexts.
- VNTRseek is publicly available for research use.
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