Entering edit mode
10 months ago
ramiro.barrantes
▴
60
ensemblVEP had a great function called parseCSQToGRanges that you could use to get the consequence information in a nice data.frame, e.g.
vcf <- readVcf(tempFile, genome="grc38")
csq <- data.frame(parseCSQToGRanges(vcf, VCFRowID=rownames(vcf)))
However, I understand that ensemblVEP is deprecated and migrated to Bioconductor::VariantAnnotation, what is the equivalent function? I can't find it!!
