Name | Long | Short | Value | Since | Description |
---|---|---|---|---|---|
EVENT_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. DEPRECATED, to be refactored (soon) | |
CHROMOSOME_SEQ |
--chr |
-c | File |
3.1 | 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). |
GENE_ID | --gid | File | 3.1 | Name and path of the GeneID parameter file with models for splice sites | |
HELP | -h | Boolean | 3.0 | Help on usage, list of parameters and corresponding descriptions | |
IN_FILE | --in | -i | File |
3.1 | Input file with reference annotation (.GTF format), MANDATORY |
IN_OPTIONS | -io | {CSS,IOK} | 3.1 | Toggle criteria for elements of the input
| |
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. DEPRECATED, to be refactored (soon) | |
OUT_EVENTS | --oev | -e | {ASE,ASI,DSP,VST} | 3.1 | Types of events that are considered:
|
OUT_EVENTS_OPT | --oeo | -v | {FLT,NMD,CP3} | 3.1 | Flags to control output options for events:
|
OUT_FILE | --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'. |
OUT_FILE_SITES | --ous | -p | File|stdout | 3.1 | Keyword 'stdout' for writing results to the standard output stream, or a fully qualified path to the output file. |
OUT_SITES | --ost | -s | {SSD,SSA,TSS,CLV,SST,SND,AUG,STP} | 3.1 | Types of sites that are output:
|
OUT_SITES_OPT | --oso | -t | {SSS} | 3.1 | Flags to control optional output for sites:
|
TMP_DIR | --tmp | File | 0.0 | The temporary directory, reads the environment variable when set to 'null'. | |
VARIANT_FILE | --vcf | File | 3.1 | Name and path of a file with the variant information (.VCF format) |