ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel...

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Hi-Plex is a PCR-based target-enrichment system for massively parallel sequencing (MPS).
• Hi-Plex ensures uniform library size for complete read-pair overlap in paired-end sequencing.
• Overlapping read pairs enable variant calling by identifying variants in both reads, filtering sequencing errors.

Purpose of the Study:

• To describe the algorithms and usage of ROVER software.
• To enable rapid and accurate genetic variant calling from specific PCR-MPS datasets.
• To facilitate the screening of genetic mutations, such as in the PALB2 gene.

Main Methods:

• ROVER software is implemented in Python for POSIX-like operating systems.
• It processes target-specific primer coordinates and aligned sequence files.
• Variants are called only when observed in both reads of overlapping read-pairs, with user-defined thresholds.

Main Results:

• ROVER enables quick and accurate identification of genetic variants.
• The software is open-source with adjustable thresholds for broad accessibility.
• It reports amplicon coverage depth for further screening identification.

Conclusions:

• ROVER facilitates rapid and accurate genetic variant calling.
• The software is suitable for a wide range of PCR-MPS users.
• It enhances the utility of overlapping paired-end MPS data for genetic analysis.