annotate_variants: annotate variants

In flow-r/ngsflows: Robust Pipelines for Next-Generation Sequencing Analysis; A Companion Package for flowr

Description

annotate variants

Usage

annotate_variants(x, outpath, outfile, execute = TRUE,
  annovarPath = "/scratch/iacs/apps/annovar/latest",
  db_path = "/scratch/iacs/apps/annovar/humandb", build = "hg19",
  protocols_g, protocols_f, chr = "contig", start = "position",
  end = "position", ref = "ref_allele", alt = "alt_allele",
  use_uuid = TRUE)

Arguments

x	A data.frame or a file with an extension recognized by read_sheet
execute	logical, run annovar dry-run
annovarPath	Path to annovar executable
db_path	path to annovar database
build	build version of the input files
protocols_g	region-type annotation databases, see Annovar's website for details
protocols_f	filter-type annotation databases, see Annovar's website for details
chr	column which represents the chromosome
start	column representing start location
end	column representing end location
ref	column representing reference allele
alt	column representing alternate allele
out_path	output path
out_file	output file

Details

Important default arguments:

-otherinfo -nastring . -remove -buildver

flow-r/ngsflows documentation built on May 16, 2019, 1:25 p.m.