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gagneurlab / MMSplice_MTSplice

Tissue-specific variant effect predictions on splicing
MIT License
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Variants without predictions #29

Closed dmb107 closed 3 years ago

dmb107 commented 4 years ago

I built the docker image based on the latest dockerfile and annotated a vcf. Around half of the variants were not annotated with a prediction score. I see the following on VEP_plugin troubleshoot section: "Some of the variants may not have prediction because they are not matched. In this case, emtpy values are returned." Could you elaborate on this issue? Is there a way for me to match the variants?

MuhammedHasan commented 4 years ago

Dear @dmb107,

MMSplice only scores splicing variants which defined as variants that in or around exons (100bp before and after exon). So remaining variants, which are not in the region of interest, will not be scored. Because, most of the case based on our data, variants in this region of interest affect splicing.

You cannot increase this match with VEP plugin. If you have a predefined set of exons or the other annotation beyond standard annotation, you may increase the matched variants with using python API. Otherwise, you cannot increase the matched variants.