merge.ides.annotation {varitas} | R Documentation |
Merge potential iDES calls with variant annotation.
Description
Merge potential iDES calls with variant annotation.
Usage
## S3 method for class 'ides.annotation'
merge(ides.filename, output = TRUE,
output.suffix = ".ann.txt",
annovar.suffix.pattern = ".annovar.hg(\\d{2})_multianno.txt")
Arguments
ides.filename |
Path to formatted iDES output (typically from convert.ides.output file) |
output |
Logical indicating whether output should be saved to file. Defaults to true. |
output.suffix |
Suffix to be appended to input filename if saving results to file |
annovar.suffix.pattern |
Suffix to match ANNOAR file |
Details
The VarDict variant calling includes a GATK call merging the call vcf file (allele frequency information etc.) with the ANNOVAR annotation, and saving the result as a table. This function is an attempt to emulate that step for the iDES calls.
Value
annotated.calls Data frame of annotations and iDES output.
[Package varitas version 0.0.2 Index]