Annovar ?missing annotation of intronic variants for splicing

[swNGS]

Dear all,
Two questions:

Annovar and annotation of splicing variants
Does anyone know how annovar annoatates a variant as splicing effect?
Is it just 'x' bases into/before an exon, or is there more to it than that?
If thats how it works, does anyone know how many bases into the exon/intron it treats as ?splicing site ?

Annotation of intronic variants with HGVS-style nomenclature.
I have not been able to get Annovar to annoate a variant more than a few bases into an intron with its appropriate HGVS-term, eg c.1234-12C>T.
Its does exonic variants fine, but I want to select variants falling with, say 20 bases before/into an exon to manually check for splicing effects (eg branch site, whcih may be further out from an intron/exon boundary than +/- 2-3 bases)
Ensembl's variant predictor tool seems to be able to annotate into the intron, just wonderd if Annovar can also.

I am using annovar with a vcf and running the summarise_annovar.pl script

Thanks,

Chris

[Heisman]

ANNOVAR by default uses an exon boundary +/- 2bp. However, you can change this value; just run the annotation script without any parameters to see all of the options and you'll see how to do this.

[swNGS]

That's very helpful. Could I just clarify if changing this parameter simply redefines what annovar assigns as a splice site, or is there a way to get it to make Annovar annotate all intronic variants by default, in addition to a pre-defined distance up/ downstream of the 1st and last exon?

[Heisman]

Pretty sure it just does all exon boundaries +/- the specified distance. That's all I know. You can simulate some variants at different locations to test this pretty easily.

[rpauly]

I have same the problem and annovar is not annotating the introns.
The above solution did not help!

Anyone has additional suggestions?