Parses a CSQ/BCSQ/ANN annotation string into a structured list of
data frames, one per transcript/consequence.
Usage
vep_parse_record(csq_value, filename, schema = NULL)
Arguments
- csq_value
Raw annotation string (pipe-delimited, comma-separated
for multiple transcripts)
- filename
Path to VCF file (for schema extraction)
- schema
Optional pre-parsed schema from vep_get_schema().
If NULL, extracted from filename.
Value
List of data frames, one per transcript. Each data frame has
one row with columns corresponding to annotation fields, properly typed.
Examples
if (FALSE) { # \dontrun{
# Get a CSQ value from a VCF
csq <- "A|missense_variant|MODERATE|BRCA1|..."
result <- vep_parse_record(csq, "annotated.vcf.gz")
result[[1]]$Consequence # "missense_variant"
result[[1]]$AF # 0.001 (numeric)
} # }