parallel_apply_BQSR_gatk: Multiregion parallelization of apply_BQSR function

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

Multiregion parallelization of apply_BQSR function

Description

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

Usage

parallel_apply_BQSR_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 = "",
  regions = NULL,
  ref_genome = "",
  rec_table = "",
  clean = TRUE,
  output_dir = ".",
  verbose = FALSE,
  tmp_dir = ".",
  batch_config = build_default_preprocess_config(),
  mode = "local",
  executor_id = make_unique("par_applyBQSR"),
  task_name = "par_applyBQSR",
  time = "48:0:0",
  threads = 4,
  ram = 4,
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

bin_samtools	REQUIRED Path to samtools executable. Default tools/samtools/samtools.
sif_gatk	REQUIRED Path to gatk executable. Default tools/gatk/gatk.
bin_picard	REQUIRED Path to picard executable. Default tools/picard/build/libs/picard.jar
bam	REQUIRED Path to the BAM file.
regions	OPTIONAL Regions to parallelize through.
ref_genome	REQUIRED Path to reference genome
rec_table	REQUIRED Path to the recalibratio table.
clean	Clean intermediary files Default TRUE
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"
executor_id	OPTIONAL Task executor name. Default "par_applyBQSR"
task_name	OPTIONAL Task name. Default "par_applyBQSR"
time	OPTIONAL If batch mode. Max run time per job. Default "48:0:0"
threads	OPTIONAL Number of threads for the main job. Default 4
ram	OPTIONAL If batch mode. RAM memory in GB per job. Default 1
update_time	OPTIONAL If batch mode. Show job updates every update time. 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.