| Name | Long | Short | Value | Since | Description |
|---|---|---|---|---|---|
| GENEID_PARAM | --gparam | File | Name and path of a file with the GeneID models for splice sites | ||
| HELP | -h | Boolean | 3.0 | Help on usage, list of parameters and corresponding descriptions | |
| INPUT | --input | -i | File | 0.0 | Input file with reference annotation (.GTF format) |
| OUTPUT | --output | -o | File|stdout | 0.0 | Keyword 'stdout' for standard output, or a path to the GTF output file |
| VARIANTS | --vcf | File | Name and path of a file with the variant information (.VCF format) |
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