[ensembl-dev] [VEP] Allele representation leading to strange annotation

[Konrad Karczewski]

Hi Will, VEP folk,

Unfortunately, allele representation has bit us once again. We have the following variant:

1       3394415 .       CGCCTCCCGGCTCTGTCCCCCCAGTCCCTCCCACTGATCTCT      TGCCTCCCGGCTCTGTCCCCCCAGTCCCTCCCACTGATCTCT,C    9533.30 PASS

Which is really a SNV that overlaps a larger deletion. VEP reads this as CGCCTCCCGGCTCTGTCCCCCCAGTCCCTCCCACTGATCTCT-> TGCCTCCCGGCTCTGTCCCCCCAGTCCCTCCCACTGATCTCT and since that sequence overlaps a splice acceptor (e.g. ENST00000378373), it marks it as a splice_acceptor_variant (even though it doesn't change the acceptor site - just tried VEP v79 on GRCh37 and same issue). Ideally, we'd put this through minimal representation (as we have implemented here: https://github.com/ericminikel/minimal_representation <https://github.com/ericminikel/minimal_representation> which nicely cuts the alleles down), but unfortunately inside a multi-sample VCF, this doesn't really work. Is there a way for this to happen inside VEP/is there a fix to this?

Thanks!
-Konrad
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