Help needed understanding VEP: Allele - the variant allele used to calculate the consequence
Hi,
Could somebody please explain me how this Allele column is computed in EnsEMBL VEP (Variant Effect Predictor)
Sample VEP output
#Uploaded_variation Location Allele Gene Feature ...
T Y:2652175 0:0 ENSG00000223773 ENST00000435581 Transcript intron_variant -/2788
T Y:2652175 6:124 - ENSR00001555882 RegulatoryFeature
I am thinking of filtering the results based on this Allele, since there are significant amount of position has 0:0. Some places the values are very high. The documentation only says
Allele - the variant allele used to calculate the consequence Thanks in advance.
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What was your input? The Allele column should display your alternative allele, so something like G or - or duplication.