multisample_mutect2_gatk: Multiregion parallelization across Mutect2 Gatk Variant...

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 across Mutect2 Gatk Variant Calling for multiple samples

Description

This function functions calls Mutect2 across multiple regions in parallel. 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

multisample_mutect2_gatk(
  sif_gatk = build_default_sif_list()$sif_gatk,
  bin_vep = build_default_tool_binary_list()$bin_vep,
  bin_bcftools = build_default_tool_binary_list()$bin_bcftools,
  bin_samtools = build_default_tool_binary_list()$bin_samtools,
  bin_bgzip = build_default_tool_binary_list()$bin_bgzip,
  bin_tabix = build_default_tool_binary_list()$bin_tabix,
  sample_sheet = NULL,
  bam_dir = "",
  normal_id = "",
  patient_id = "",
  pattern = "bam$",
  ref_genome = build_default_reference_list()$HG19$reference$genome,
  germ_resource = build_default_reference_list()$HG19$variant$germ_reference,
  biallelic_db = build_default_reference_list()$HG19$variant$biallelic_reference,
  db_interval = build_default_reference_list()$HG19$variant$biallelic_reference,
  pon = build_default_reference_list()$HG19$panel$PCF_V3$variant$pon_muts,
  chr = c(1:22, "X", "Y", "MT"),
  method = "single",
  regions = NULL,
  output_dir = ".",
  verbose = FALSE,
  filter = TRUE,
  annotate = TRUE,
  extract_pass = TRUE,
  orientation = TRUE,
  mnps = FALSE,
  contamination = TRUE,
  clean = FALSE,
  header = TRUE,
  sep = "\t",
  batch_config = build_default_preprocess_config(),
  threads = 4,
  ram = 8,
  mode = "local",
  executor_id = make_unique_id("multiSampleMutect2"),
  task_name = "multiSampleMutect2",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

sif_gatk	REQUIRED Path to gatk sif file.
bin_vep	REQUIRED Path to VEP binary.
bin_bcftools	REQUIRED Path to bcftools binary file.
bin_samtools	REQUIRED Path to samtools binary file.
bin_bgzip	REQUIRED Path to bgzip binary file.
bin_tabix	REQUIRED Path to tabix binary file.
sample_sheet	OPTIONAL Path to sheet with sample information.
bam_dir	OPTIONAL Path to directory with BAM files.
normal_id	OPTIONAL Path to directory with BAM files.
ref_genome	REQUIRED Path to reference genome fasta file.
germ_resource	REQUIREDPath to germline resources vcf file.
pon	OPTIONAL Path to panel of normal.
chr	OPTIONAL Chromosomes to analyze. Default c(1:22,"X","Y","MT")
method	OPTIONAL Default variant calling method. Default single. Options "single","multi"
regions	OPTIONAL Regions to analyze. If regions for parallelization are not provided then these will be infered from BAM file.
output_dir	OPTIONAL Path to the output directory.
verbose	OPTIONAL Enables progress messages. Default False.
filter	OPTIONAL Filter Mutect2. Default TRUE.
orientation	OPTIONAL Produce read orientation inforamtion. Default FALSE
mnps	OPTIONAL Report MNPs in vcf file.
contamination	OPTIONAL Produce sample cross-contamination reports. Default TRUE.
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.
output_name	OPTIONAL Name for the output. If not given the name of one of the samples will be used.

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.