index_vcf_htslib: Index VCF using TABIX 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

Index VCF using TABIX from HTSLIB

Description

Index VCF using TABIX from HTSLIB

Usage

index_vcf_htslib(
  bin_tabix = build_default_tool_binary_list()$bin_tabix,
  vcf = NULL,
  ...
)

Arguments

bin_tabix	Path to TABIX executable.
vcf	Path to the input VCF file.
index_format	Indexing method. Default tbi. Options tbi,csi
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 "indexVCF"
task_name	OPTIONAL Task name. Default "indexVCF"
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.