Similar posts have been put up in the past by other users but I haven't yet found any helpful answers.
Are there annotation tools out there that annotate variants located in the canonical splice sites? SnpEff seems to annotate them only as "intronic". Ensembl Variant effect predictor shows some annotation as "missense_variant&splice_region_variant" , but spot-checked variants do not always fall in splice regions - the documentation does not provide more info either on splice region designation.
I have a VCF with a list of 50000 variants, so am hoping to find some tools for higher-throughput annotation. Any suggestion ? Great many thanks.