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Ensembl / ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
https://www.ensembl.org/vep
Apache License 2.0
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SpliceAI plugin update please #1726

Closed xiucz closed 3 months ago

xiucz commented 4 months ago

Hi,

VEPversion: 105

Is there a plan to update the SpliceAI plugin? I noticed a significant difference between the results from VEP-SpliceAI and other software（https://github.com/broadinstitute/SpliceAI-lookup and https://github.com/Illumina/SpliceAI）. The results from Illumina-SpliceAI/VEP-spliceAI are the same but differ from those mentioned in the paper. When I updated the SpliceAI database to gencode v44, the results aligned with SpliceAI-lookup and the paper. However, the database used by VEP-spliceAI is relatively old. Do you have any plans to update it?

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Best, xiucz

jamie-m-a commented 4 months ago

Hi @xiucz

Thanks for you're query. Our current plan for rerunning SpliceAI is tied to changes in the MANE Select transcript set, rather than updates to gencode, hence we have not generated newer files recently. If/when there is an update to the MANE Select set we will look to generate new spliceAI scores.