Name | Long | Short | Value | Since | Description |
---|---|---|---|---|---|
DIMENSION | --dim | -k | Integer | 0.0 | Dimension of the AS events to be extracted, Default is 2 (i.e. 'pairwise events'), and values < 2 stand for 'complete' events <TM> |
EDGE_CONFIDENCE | --ec | Integer | 2.2 | Level of confidence for edges (i.e., annotated transcription starts/poly-adenylation sites). The default is to trust no annotated edge and to extend overlapping first/last exons of a transcript to their most extreme position:
All transcript edges of confidence level > edgeConfidence are extended in case the annotation shows another exon with the same adjacent splice site and an earlier/later start/end. | |
EVENTS | --events | -e | {ASE,ASI,DSP,VST} | 3.0 | Types of events that are considered:
|
GENOME | --genome | -g | File | 2.2 | Path to a folder with genomic sequences, one per chromosome (.FASTA format). The header tags of each chromosome have to coincide with the <seqname> field ($1) of the annotation (GTF file). |
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 | |
INOPTIONS | -io | {CSS,IOK} | 3.1 | Toggle criteria for elements of the input
| |
INPUT | --in | -i | File | 0.0 | Input file with reference annotation (.GTF format), MANDATORY |
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:
All introns in transcripts of confidence level > threshold are discarded. | |
OUTOPTIONS | --oo | {FLT,NMD,CP3} | 3.1 | Flags to control output options for events:
| |
OUTPUT | --out | -o | File|stdout | 0.0 | Keyword 'stdout' for writing results to the standard output stream, or a fully qualified path to the output file. The parameter is optional--if nothing is specified, the output will be written to a file '<input file>_astalavista.gtf.gz'. |
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) |