analyze_covariates_gatk: Wrapper of AnalyzeCovariates function in gatk

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

Wrapper of AnalyzeCovariates function in gatk

Description

Generates a report of the recalibrated values. This function wraps around gatk AnalyzeCovariates function. For more information about this function: https://gatk.broadinstitute.org/hc/en-us/articles/360037066912-AnalyzeCovariates

Usage

analyze_covariates_gatk(
  sif_gatk = build_default_sif_list()$sif_gatk,
  before = "",
  after = "",
  output_dir = ".",
  verbose = FALSE,
  tmp_dir = ".",
  batch_config = build_default_preprocess_config(),
  threads = 4,
  ram = 4,
  mode = "local",
  executor_id = make_unique_id("recalCovariates"),
  task_name = "recalCovariates",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

sif_gatk	REQUIRED Path to gatk executable. Default tools/gatk/gatk.
before	REQUIRED Recalibration table produced by generate_BQSR function.
after	OPTIONAL Recalibration table produced by generate_BQSR function.
output_dir	OPTIONAL Path to the output directory.
verbose	OPTIONAL Enables progress messages. Default False.
tmp_dir	OPTIONAL Path to the temporary directory.
threads	OPTIONAL Number of threads to split the work. Default 4
ram	OPTIONAL RAM memory to asing to each thread. Default 4
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"
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.