apply_BQSR_gatk: Wrapper of applyBQSR function 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 applyBQSR function gatk

Description

Applies numerical corrections to each individual basecall based on the covariates analyzed before. This function wraps around gatk applyBQSR function. For more information about this function: https://gatk.broadinstitute.org/hc/en-us/articles/360050814312-ApplyBQSR

Usage

apply_BQSR_gatk(
  region = "",
  rdata = NULL,
  selected = NULL,
  sif_gatk = build_default_sif_list()$sif_gatk,
  bam = "",
  ref_genome = "",
  rec_table = "",
  output_dir = ".",
  verbose = FALSE,
  tmp_dir = ".",
  batch_config = build_default_preprocess_config(),
  mode = "local",
  threads = 4,
  ram = 4,
  executor_id = make_unique_id("applyBQSR"),
  task_name = "applyBQSR",
  time = "48:0:0",
  update_time = 60,
  wait = TRUE,
  hold = NULL
)

Arguments

sif_gatk	REQUIRED Path to gatk executable. Default tools/gatk/gatk.
bam	REQUIRED Path to the BAM file.
ref_genome	REQUIRED Path to reference genome
rec_table	REQUIRED Path to covariates table generated by generate_BSQR.
output_dir	OPTIONAL Path to the output directory.
verbose	OPTIONAL Enables progress messages. Default False.
tmp_dir	OPTIONAL Path to the temporary directory.
mode	REQUIRED Where to parallelize. Default local. Options "local","batch"
threads	Number of threads to split the work. Default 3
ram	OPTIONAL If batch mode. RAM memory in GB per job. Default 1
executor_id	OPTIONAL Task executor name. Default "applyBQSR"
task_name	OPTIONAL Task name. Default "applyBQSR"
time	OPTIONAL If batch mode. Max run time per job. Default "48:0:0"
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.