VCFvariance.pl

VCFvariance.pl infers polyploidy and heterokaryosis from low-coverage whole-genome sequencing data by analyzing the variance of allele balance.

Key Features:

• Low-Coverage Requirement: Operates on whole-genome sequencing data at coverage as low as 10x, contrasted with traditional methods that require >50x coverage.
• Single-Value Reduction: Reduces the allele balance profile to a single scalar value to facilitate determination of two or more haplotypes.
• Variance-Based Metric: Uses the variance of allele balance as the primary metric to detect deviations from a diploid state.
• Validation and Application: Validated on simulated, synthetic, and authentic read sets from oomycetes, fungi, and plants, and applied to studies of Bremia lactucae and Phytophthora infestans.
• Implementation: Implemented as a Perl script for integration into computational workflows.

Scientific Applications:

• Polyploidy Detection: Infers polyploidy by identifying variance patterns in allele balance that deviate from diploid expectations.
• Heterokaryosis Identification: Identifies heterokaryosis by detecting multiple coexisting haplotypes within single organisms, relevant to fungi and plant pathogens.
• Genome-status Inference in Pathogens: Applied to assess genome complexity and status in pathogens such as Bremia lactucae and Phytophthora infestans.

Methodology:

Calculates the variance of allele balance from sequencing data, reduces the allele-balance profile to a single value, and interprets deviations from diploid expectations as evidence of additional haplotypes; implemented as a Perl script and applicable to low-coverage (≈10x) whole-genome data.