annovar_annotate_region: Annotate variant regions

In imbs-hl/imbs: Collection of functions used at the IMBS

Description

Annotate variant regions

Usage

annovar_annotate_region(avinput.file, output.prefix,
  db.path = "/imbs/external_data/annotation_and_references/annovar/humandb",
  build = "hg19", exec = "annotate_variation.pl")

Arguments

avinput.file	[string] The file name of the ANNOVAR input file.
output.prefix	[string] The basename of the output files.
db.path	[string] The path to the database files. Default is /imbs/external_data/annotation_and_references/annovar/humandb.
build	[string] Human genome build code. Default is 'hg19'.
exec	[string] Path to annotate_variation script.

Details

Use ANNOVAR to find if variants hit exons or hit intergenic regions, or hit introns, or hit a non-coding RNA genes.

Value

Captured system output as character vector.

imbs-hl/imbs documentation built on Sept. 6, 2019, 11:05 p.m.