merge.ides.annotation: Merge potential iDES calls with variant annotation.

In varitas: Variant Calling in Targeted Analysis Sequencing Data

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.

varitas documentation built on Nov. 14, 2020, 1:07 a.m.