Tools for working with genomic and high throughput sequencing data.
Group: FASTA
Updates the sequence names in an Interval List file.
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.
| Name | Flag | Type | Description | Required? | Max # of Values | Default Value(s) |
|---|---|---|---|---|---|---|
| input | i | PathToIntervals | Input interval list. | Required | 1 | |
| dict | d | PathToSequenceDictionary | The path to the sequence dictionary with contig aliases. | Required | 1 | |
| output | o | PathToIntervals | Output interval list. | Required | 1 | |
| skip-missing | Boolean | Skip missing source contigs. | Optional | 1 | false |