search

UW-GAC / wgsaparsr

Code for parsing TOPMED variant annotation files produced by the WGSA annotation tool.
Other
5 stars 3 forks source link

readme

DOI

Service Master Develop
CI Status Travis-CI Build Status Travis-CI Build Status
Test Coverage Coverage Status Coverage Status

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()