diff --git a/docs/commands/cis-splice-effects-associate.md b/docs/commands/cis-splice-effects-associate.md index faf8abc..2c5f3c9 100644 --- a/docs/commands/cis-splice-effects-associate.md +++ b/docs/commands/cis-splice-effects-associate.md @@ -22,7 +22,6 @@ The `cis-splice-effects associate` command is used to identify splicing misregul | -o STR | Output file containing the aberrant splice junctions with annotations. [STDOUT] | | -v STR | Output file containing variants annotated as splice relevant (VCF format). | | -j STR | Output file containing the aberrant junctions in BED12 format. | -| -s INT | Strand specificity of RNA library preparation, where 0 = unstranded/XS, 1 = first-strand/RF, 2 = second-strand/FR. This option is required. If your alignments contain XS tags, these will be used in the "unstranded" mode. | | -w INT | Window size in b.p to associate splicing events in. The tool identifies events in variant.start +/- w basepairs. Default behaviour is to look at the window between previous and next exons. | | -e INT | Maximum distance from the start/end of an exon to annotate a variant as relevant to splicing, the variant is in exonic space, i.e a coding variant. [3] | | -i INT | Maximum distance from the start/end of an exon to annotate a variant as relevant to splicing, the variant is in intronic space. [2] |