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 column.
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
metadata column is included in the result that maps back to the row
(variant) in the original VCF. This option is only applicable when the
info.key field has data (is not empty).
info.key column is found the function returns the data in
GRanges object with consequence data as the
metadata columns. If no 'CSQ' column is found the
rowRanges() is returned.
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=VEPFlags(flags=list(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]
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