| Name | Long | Short | Value | Since | Description |
|---|---|---|---|---|---|
| COMPLETE3 | --complete3 | Boolean | 2.2 | Require 3'-complete transcripts | |
| DIMENSION | --dimension | -k | Integer | 0.0 | Dimension of the AS events to be extracted, values < 2 stand for 'complete' events <TM> |
| EVENTS | --events | -e | {ASExt,ASInt,DS,VS} | 3.0 | Types of events that are considered |
| GENOME | --genome | -g | File | 2.2 | Folder with genomic sequences, one per chromosome (.FASTA format) |
| GENEID_PARAM | --gparam | File | 3.1 | 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) |
| INTRON_CONFIDENCE | --ic | Integer | 2.2 | Level of intron confidence, below which introns are trusted without checks. The default is to trust all introns (i.e., ic= 255). Introns are assigned a confidency class:
| |
| NMD | --nmd | 2.2 | Check nonsense-mediated decay conditions | ||
| OUTPUT | --output | -o | File|stdout | 0.0 | Keyword 'stdout' for standard output, or an abstract path to the output file |
| TMP_DIR | --tmp | File | 0.0 | The temporary directory, reads the environment variable when set to 'null'. | |
| VARIANTS | --vcf | File | 3.1 | Name and path of a file with the variant information (.VCF format) |
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