parse_to_file: Parse the WGSA output file to tidy and select columns of...

In UW-GAC/wgsaparsr: A R package for Parsing Annotation File for Database Import

Description

WGSA generates distinct annotation output files for annotating indel or SNVs. These output files contain thousands of fields, including fields with lists of entries. parse_to_file() reads a WGSA output file in chunks, parses the chunks, writes to two output files - one for the snv or indel annotation, and another for the dbnsfp annotation. These tab-separated output files can then be imported to a database for aggregation, or used for obtaining variant annotation.

Usage

parse_to_file(source_file, config, destination = NA,
  dbnsfp_destination = NA, chunk_size = 10000, header_file = NA,
  verbose = TRUE)

Arguments

source_file	Path to the WGSA output file to parse (indel or SNV annotation)
config	Path to config file or a dataframe that passes validate_config()
destination	Path to the desired indel or snv output file
dbnsfp_destination	Path to the desired dbnsfp output file
chunk_size	Number of lines to parse each iteration (default 10,000)
header_file	Path to a header file (optional)
verbose	more output to screen (default TRUE)

Examples

## Not run: 

parse_to_file(source_file = "WGSA_chr_1.gz",
 destination = "parsed_chr_1_snv.tsv",
 dbnsfp_destination = "parsed_chr_1_dbnsfp.tsv",
 chunk_size = 1000)

## End(Not run)

UW-GAC/wgsaparsr documentation built on Aug. 9, 2020, 5:50 a.m.