timd1/vcfdist repository overview

vcfdist is a distance-based variant calling evaluation tool that:

• simultaneously evaluates SNPS, small INDELs, complex, tandem repeat, and structural variants
• gives partial credit to variant calls which are mostly correct
• standardizes query and truth VCF variants to a consistent representation
• requires local phasing of both input VCFs and enforces correct local phasing of variants
• discovers long-range variant representation dependencies using a novel clustering algorithm
• works on monoploid and diploid VCF contigs

This results in more stable SNP and INDEL precision-recall curves than previous work, particularly for complex variants. vcfdist also reports alignment distance based metrics for evaluation which are entirely independent of variant representation, providing greater insight into variant calling performance.

This project is currently under active development. We welcome the submission of any feedback, issues, or suggestions for improvement!