variants_by_filters_vcf: Removes variants with from VCF file vased on the values in...

In TearsWillFall/ULPwgs: An implementation of a wrapper for estimating tumor fraction in ultra-low-pass whole genome sequencing (ULP-WGS) for cell-free DNA in GNU/Unix based systems

Removes variants with from VCF file vased on the values in the FILTER column

Description

VCF datastructure is in list format and contains a header, a body and the corresponding col_names

Usage

variants_by_filters_vcf(
  bin_bgzip = build_default_tool_binary_list()$bin_bgzip,
  bin_tabix = build_default_tool_binary_list()$bin_tabix,
  vcf = NULL,
  filters = "PASS",
  exclusive = FALSE,
  chromosomes = NULL,
  ...
)

Arguments

bin_bgzip	Path to bgzip executable.
bin_tabix	Path to TABIX executable.
vcf	Path to the input VCF file.
filters	Filters to filter VCF by. Default PASS
exclusive	Only keep variants with exactly these filters. Default TRUE.
output_name	Output file name.
compress	Compress VCF file. Default TRUE.
index	Index VCF file. Default TRUE.
index_format	VCF index format. Default tbi. Options tbi,cbi.
bgzip_index	Create BGZIP index for compressed file. Default FALSE
output_dir	Path to the output directory.
clean	Remove input VCF after completion. Default FALSE.
verbose	Enables progress messages. Default False.
executor_id	Task EXECUTOR ID. Default "gatherBQSR"
task_name	Task name. Default "gatherBQSR"
mode	REQUIRED Where to parallelize. Default local. Options "local","batch"
time	OPTIONAL If batch mode. Max run time per job. Default "48:0:0"
threads	Number of threads to split the work. Default 3
ram	OPTIONAL If batch mode. RAM memory in GB per job. Default 1
update_time	OPTIONAL If batch mode. Show job updates every update time. Default 60
wait	OPTIONAL If batch mode wait for batch to finish. Default FALSE
hold	OPTIONAL HOld job until job is finished. Job ID.

TearsWillFall/ULPwgs documentation built on April 18, 2024, 3:45 p.m.