SVrefine¶
SVrefine reads a delta-formatted file of MUMmer alignments of an assembly to the reference to call structural variants (or refine variants in chosen genomic regions) and print them out in VCF format.
Usage¶
SVrefine.pl --delta <path to delta file of alignments> --regions <path to BED-formatted file of regions> --ref_fasta <path to reference multi-FASTA file> --query_fasta <path to query multi-FASTA file> --outvcf <path to output VCF file> --svregions <path to output BED file of SV regions> --outref <path to bed file of homozygous reference regions> --nocov <path to bed file of regions with no coverage>
Options¶
| Option | Description |
|---|---|
| –help|–manual | Display documentation. |
| –delta | Path to a delta file produced by MUMmer with alignments to be used for retrieving SVs. |
| –regions | Path to a BED file of regions to be investigated for structural variants in the assembly (Optional). |
| –ref_fasta | Path to a multi-fasta file containing the sequences used as a reference in the MUMmer alignment (Optional). |
| –query_fasta | Path to a multi-fasta file containing the sequences used as a query in the MUMmer alignment (Optional). |
| –outvcf | Path to which to write a new VCF-formatted file of structural variants. |
| –refname | String to include as the reference name in the VCF header. |
| –samplename | String to include as the sample name in the output VCF file. |
| –maxsize | Specify an integer for the maximum size of SV to report. |
| –noheader | Flag option to suppress printout of the VCF header. |
| –nocov | Path to write a BED file with “no coverage” regions (only used when –regions option is specified). |