Parse the CSQ column in a VCF object returned from the Ensembl Variant Effect Predictor (VEP).
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The name of the INFO key that VEP writes the consequences to in the output
Arguments passed to other methods. Currently not used.
ensemblVEP returns a
VCF object, the
consequence data are returned unparsed in the 'CSQ' INFO
parseCSQToGRanges parses these data into a
GRanges object that is expanded to match the dimension
of the 'CSQ' data. Because each variant can have multiple
matches, the ranges in the
GRanges are repeated.
If rownames from the original VCF are provided as
VCFRowID a metadata column is included in the result
that maps back to the row (variant) in the original VCF.
GRanges object with consequence data as the
Ensembl VEP Home: http://uswest.ensembl.org/info/docs/tools/vep/index.html
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file <- system.file("extdata", "ex2.vcf", package="VariantAnnotation") vep <- ensemblVEP(file, param=VEPParam(dataformat=c(vcf=TRUE))) ## The returned 'CSQ' data are unparsed. info(vep)$CSQ ## Parse into a GRanges and include the 'VCFRowID' column. vcf <- readVcf(file, "hg19") csq <- parseCSQToGRanges(vep, VCFRowID=rownames(vcf)) csq[1:4]