Synopsis

The cis-splice-effects identify command is used to identify splicing misregulation events. This command takes in a list of variants in the VCF format and RNAseq alignments produced with a splice-aware aligner in the BAM format. The tool then proceeds to identify non-canonical splicing junctions near the variant sites.

Usage

regtools cis-splice-effects identify [options] variants.vcf alignments.bam ref.fa annotations.gtf

Input

Input Description
variants.vcf Variant call in VCF format from which to look for cis-splice-effects.
alignments.bam Aligned RNAseq BAM produced with a splice aware aligner, that has been indexed for example with samtools index. We have tested this command with alignments from TopHat.
ref.fa The reference FASTA file. The donor and acceptor sequences used in the "splice-site" column of the annotated junctions are extracted from the FASTA file.
annotations.gtf The GTF file specifies the transcriptome that is used to annotate the junctions and variants. For examples, the Ensembl GTFs for release78 are here.

Note - Please make sure that the version of the annotation GTF that you use corresponds with the version of the assembly build (ref.fa) and that the co-ordinates in the VCF file are also from the same build.

Options

Option Description
-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 (0 = unstranded, 1 = first-strand/RF, 2, = second-strand/FR). [1]
-w INT Window size in b.p to identify 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]
-I Annotate variants in intronic space within a transcript(not to be used with -i).
-E Annotate variants in exonic space within a transcript(not to be used with -e).
-S Don't skip single exon transcripts.

Output

For an explanation of the annotated junctions that are identified by this command please refer to the output of the junctions annotate command here For an explanation of the annotated variants that are identified by this command when using the -v option, please refer to the output of the variants annotate command here

Examples

cis-splice-effects identify example