SVcomp¶
SVcomp calculates “distances” between pairs of structural variants in VCF format by constructing their alternate haplotypes and aligning them to each other.
Usage¶
svanalyzer comp --ref reference.fasta --first <first VCF-formatted file> --second <second VCF-formatted file>
Options¶
| 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 |