compress_and_index_bed_htslib: Compress BED using BGZIP from HTSLIB

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

Compress BED using BGZIP from HTSLIB

Description

Compress BED using BGZIP from HTSLIB

Usage

compress_and_index_bed_htslib(
  bin_bgzip = build_default_tool_binary_list()$bin_bgzip,
  bin_tabix = build_default_tool_binary_list()$bin_tabix,
  bed = NULL,
  compress = TRUE,
  index = TRUE,
  ...
)

Arguments

bin_bgzip	Path to bgzip executable.
bin_tabix	Path to TABIX executable.
bed	Path to the input VCF file.
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_name	Output file name.
output_dir	Path to the output directory.
clean	Remove input VCF after completion. Default FALSE.
verbose	Enables progress messages. Default False.
batch_config	Default config to use in BATCH mode.
ram	RAM memory to use in GB. Default 4.
tmp_dir	Path to TMP directory. Default .
executor_id	OPTIONAL Task executor name. Default "compressVCF
task_name	OPTIONAL Task name. Default "compressVCF"
time	OPTIONAL If batch mode. Max run time per job. Default "48:0:0"
update_time	OPTIONAL If batch mode. Job update time in seconds. 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.