Code for parsing TOPMED variant annotation files produced by the WGSA annotation tool.
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wgsaparsr

This package is the code the TOPMED DCC uses to parse genetic variant annotation files produced by the WGSA annotation tool

Installation

You can install wgsaparsr from github with:

# install.packages("devtools") 
devtools::install_github("UW-GAC/wgsaparsr")

Example

# list all fields in an annotation file: 
all_fields <- get_fields("WGSA_chr_1.gz")

# load a configuration file
local_config <- load_config("config.tsv")

# parse WGSA output file tsv output files 
# (one for dbnsfp annotations, one for snv/indel annotaitons)
parse_to_file(source_file = snv_source_file,
  destination = snv_destination,
  dbnsfp_destination = dbnsfp_destination,
  config = config,
  freeze = 5,
  chunk_size = 1000,
  verbose = TRUE)

Expanded configuration file documentation coming soon. In the meantime, see ?wgsaparsr::load_config()