tabulate_vcf: Generate tabulated table from annotate VCF

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

Generate tabulated table from annotate VCF

Description

VCF datastructure with tabulated INFO column body

Usage

tabulate_vcf(
  vcf = NULL,
  tumour_id = NULL,
  normal_id = NULL,
  patient_id = NULL,
  chromosomes = NULL,
  ...
)

Arguments

vcf	Path to VCF file
output_dir	Path to the output directory.
threads	OPTIONAL Number of threads to split the work. Default 4
ram	OPTIONAL RAM memory to asing to each thread. Default 4
verbose	OPTIONAL Enables progress messages. Default False.
mode	REQUIRED Where to parallelize. Default local. Options "local","batch"
executor_id	Task EXECUTOR ID. Default "recalCovariates"
task_name	Task name. Default "recalCovariates"
time	OPTIONAL If batch mode. Max run time per job. Default "48:0:0"
hold	OPTIONAL HOld job until job is finished. Job ID.

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