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) |