mutect2_gatk: Variant Calling using Mutect2

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

Variant Calling using Mutect2

Description

This function functions calls Mutect2 for variant calling. If a vector of tumour samples are provided these will be processed in multi-sample mode. To run in tumour-normal mode suppply a single tumour and normal sample. If no normal is supplied this will run in tumour only. TO DO// Implement mitochondrial mode feature

Usage

mutect2_gatk(
  region = "",
  rdata = NULL,
  selected = NULL,
  sif_gatk = build_default_sif_list()$sif_gatk,
  tumour = "",
  normal = NA,
  output_name = "",
  ref_genome = build_default_reference_list()$HG19$reference$genome,
  germ_resource = build_default_reference_list()$HG19$variant$germ_reference,
  pon = "",
  output_dir = ".",
  tmp_dir = ".",
  verbose = FALSE,
  orientation = FALSE,
  mnps = FALSE,
  batch_config = build_default_preprocess_config(),
  threads = 4,
  ram = 4,
  mode = "local",
  executor_id = make_unique_id("Mutect2"),
  task_name = "Mutect2",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

rdata	OPTIONAL Import R data information with list of BAM.
selected	OPTIONAL Select BAM from list.
sif_gatk	REQUIRED Path to gatk sif file.
tumour	REQUIRED Path to tumour BAM file.
normal	OPTIONAL Path to normal BAM file.
output_name	OPTIONAL Name for the output. If not given the name of the first tumour sample of the samples will be used.
ref_genome	REQUIRED Path to reference genome fasta file.
germ_resource	REQUIREDPath to germline resources vcf file.
pon	OPTIONAL Path to panel of normal.
output_dir	OPTIONAL Path to the output directory.
verbose	OPTIONAL Enables progress messages. Default False.
orientation	OPTIONAL Produce read orientation inforamtion. Default FALSE
mnps	OPTIONAL Report MNPs in vcf file.
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.
contamination	OPTIONAL Produce sample cross-contamination reports. Default TRUE.

Details

For more information read: https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2

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