SVcomp calculates “distances” between pairs of structural variants in VCF format by constructing their alternate haplotypes and aligning them to each other.


svanalyzer comp --ref reference.fasta --first <first VCF-formatted file> --second <second VCF-formatted file>


Option Description
–help|–manual Display documentation.
–ref The reference FASTA file for the supplied VCF file or files.
–first A VCF-formatted file of variants to compare
–second Second VCF-formatted file of variants to compare–must have the same number of variants as the first file