VCF2CNA: A tool for efficiently detecting copy-number alteration in VCF genotype data

VCF2CNA is a web interface tool for copy-number alteration (CNA) analysis of VCF and other variant file formats. We applied it to 46 adult glioblastoma and 146 pediatric neuroblastoma samples sequenced by Illumina and Complete Genomics (CGI) platforms respectively. VCF2CNA was highly consistent with a state-of-the-art algorithm using raw sequencing data (mean F1-score=0.994) in high-quality glioblastoma samples and was robust to uneven coverage introduced by library artifacts. In the neuroblastoma set, VCF2CNA identified MYCN high-level amplifications in 31 of 32 clinically validated samples compared to 15 found by CGIs HMM-based CNA model. The findings suggest that VCF2CNA is an accurate, efficient and platform-independent tool for CNA analyses without accessing raw sequence data.