parallel_generate_BQSR_gatk: Multiregion parallelization of generate_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 generate_BQSR function

Description

Generates a recalibration table based on various covariates. This function wraps around gatk BaseRecalibrator function. For more information about this function: https://gatk.broadinstitute.org/hc/en-us/articles/360036898312-BaseRecalibrator

Usage

parallel_generate_BQSR_gatk(
  bin_samtools = build_default_tool_binary_list()$bin_samtools,
  sif_gatk = build_default_sif_list()$sif_gatk,
  bam = "",
  regions = NULL,
  ref_genome = "",
  clean = TRUE,
  dbsnp = "",
  tmp_dir = ".",
  threads = 3,
  ram = 4,
  executor_id = make_unique_id("par_generateBQSR"),
  task_name = "par_generateBQSR",
  output_dir = ".",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  mode = "local",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

bin_samtools	REQUIRED Path to gatk executable. Default tools/samtools/samtools.
sif_gatk	REQUIRED Path to gatk executable. Default tools/gatk/gatk.
bam	REQUIRED Path to the BAM file.
regions	OPTIONAL Regions to parallelize through.
ref_genome	REQUIRED Path to reference genome
clean	Remove intermediary files. Default TRUE
dbsnp	REQUIRED Path to known snp positions in VCF format. Multiple vcf can be supplied as a vector.
tmp_dir	OPTIONAL Path to the temporary directory.
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	Task EXECUTOR ID. Default "par_generateBQSR"
task_name	Task name. Default "par_generateBQSR"
output_dir	OPTIONAL Path to the output directory.
verbose	OPTIONAL Enables progress messages. Default False.
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. 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.