Tools for working with genomic and high throughput sequencing data.
Group: VCF/BCF
Updates then contig names in a VCF.
The name of each sequence must match one of the names (including aliases) in the given sequence dictionary. The new name will be the primary (non-alias) name in the sequence dictionary.
Use --skip-missing to ignore variants where a contig name could not be updated (i.e. missing from the sequence dictionary).
| Name | Flag | Type | Description | Required? | Max # of Values | Default Value(s) |
|---|---|---|---|---|---|---|
| input | i | PathToVcf | Input VCF. | Required | 1 | |
| dict | d | PathToSequenceDictionary | The path to the sequence dictionary with contig aliases. | Required | 1 | |
| output | o | PathToVcf | Output VCF. | Required | 1 | |
| skip-missing | Boolean | Skip contigs in the VCF that are not found in the sequence dictionary. | Optional | 1 | false |