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Old 04-30-2014, 12:21 PM   #1
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Location: Brazil

Join Date: May 2013
Posts: 8
Question Some help with Variant Effect Predictor (VEP)

Hi guys,

I've run the VEP tool and got some results that don't make sense when I checked the allele used to calculate the consequence associate with the strand, like below:

substitution # allele used to calculate consequence # strand
C/T # T # +
G/T # T # -
C/T # A # +
A/C # G # -

Reading the tutorial I've undestood that when the strand is (+) the alllele used to calculate the consequence would be itself; when the strand is (-) the allele used would be the complementar nucleotide. Am I wrong? Why these contraditory results?

Thank you all for any help
moredd is offline   Reply With Quote

contraditory results, snp annotation, vep

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