recal_gatk: Function for base quality recalibration

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

Function for base quality recalibration

Description

This function recalibrates the base quality of the reads in two steps process based on GATK best practices guides.

Usage

recal_gatk(
  bin_samtools = build_default_tool_binary_list()$bin_samtools,
  sif_gatk = build_default_sif_list()$sif_gatk,
  bin_picard = build_default_tool_binary_list()$bin_picard,
  bam = "",
  ref_genome = "",
  dbsnp = "",
  ram = 4,
  threads = 4,
  output_dir = ".",
  tmp_dir = ".",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  executor_id = make_unique_id("recalGATK"),
  task_name = "recalGATK",
  clean = TRUE,
  mode = "local",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

bin_samtools	REQUIRED Path to picard executable. Default path tools/samtools/samtools.
sif_gatk	REQUIRED Path to picard executable. Default path tools/gatk/gatk.
bin_picard	REQUIRED Path to picard executable. Default path tools/picard/build/libs/picard.jar.
bam	REQUIRED Path to BAM file.
ref_genome	REQUIRED Path to reference genome.
dbsnp	REQUIRED Known variant database.Requires atleast 1.
ram	OPTIONAL RAM memory per thread.
threads	OPTIONAL Number of threads to split the work.
output_dir	OPTIONAL Path to the output directory.
tmp_dir	OPTIONAL Path to the temporary directory.
verbose	OPTIONAL Enables progress messages. Default False.#
executor_id	Task EXECUTOR ID. Default "recalGATK"
clean	Clean input files. Default TRUE.
mode	REQUIRED Where to parallelize. Default local. Options "local","batch"
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.
task_id	Task nam. Default "recalGATK"

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