Splice junction SNPs

Question

[rbronste]

Hi, wondering if anyone knows of a tool/method for assaying the overlap between splice junctions/sites and SNPs outside of manual curation? Thanks.

[Pierre Lindenbaum]

annotate with VEP, snpEff , etc... ?

Answer 1

[Jeremy Leipzig]

most of the SNPs that alter splicing (sQTLs) are not directly at the splice junctions but nearby, so just identifying the ones right at the junction might not be that biologically relevant https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0030099