RAPTR-SV

RAPTR-SV detects structural variants in paired-end whole-genome sequencing (WGS) data using read-pair and split-read evidence to identify tandem duplications and other SVs.

Key Features:

• Sensitivity and precision: Recovered 66.4% of simulated tandem duplications with 99.2% precision in simulations.
• Read-evidence methods: Leverages read-pair and split-read analysis by examining spatial relationships of reads that map unexpectedly far apart or to unexpected genomic regions.
• Benchmarking: When compared to Delly and LUMPY on 1000 Genomes Project datasets, it identified twice as many tandem duplications as Delly while producing approximately 85% fewer duplication predictions.
• Implementation: Implemented in Java and utilizes the Java 8 collections framework.

Scientific Applications:

• Structural variant discovery in WGS: Accurate detection of tandem duplications and other SVs for genome-wide analyses of structural variation.
• Large-scale genomic studies: Reduction of false positives to lessen downstream validation burden in population and clinical WGS projects.
• Genetic diversity and disease research: Investigation of structural variation contributions to genetic diversity and disease mechanisms.

Methodology:

Uses read-pair and split-read computational methods to analyze mapping distance and orientation of paired reads; evaluated by simulations and by comparison to Delly and LUMPY using 1000 Genomes Project datasets; implemented in Java (Java 8 collections framework).