Name | Long | Short | Value | Since | Description |
---|---|---|---|---|---|
DIMENSION | --dimension | -k | Integer | 0.0 | Dimension of the AS events to be extracted, values < 2 stand for 'complete' events <TM> |
GENOME | --genome | -g | File | 0.0 | Folder with genomic sequences, one per chromosome (.FASTA format) |
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 an abstract path to the output file |
VARIANTS | --vcf | File | Name and path of a file with the variant information (.VCF format) |