create_pon_gatk: Wrapper around CreateSomaticPanelOfNormals from GATK package

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

Wrapper around CreateSomaticPanelOfNormals from GATK package

Description

This function creates a somatic panel of normals from normal samples bam files. Recommended minimum number of normal samples is around 40.

Usage

create_pon_gatk(
  sif_gatk = build_default_sif_list()$sif_gatk,
  bin_bcftools = build_default_tool_binary_list()$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()$bin_tabix,
  output_name = "PoN",
  vcfs = "",
  regions = NULL,
  output_dir = ".",
  ref_genome = build_default_reference_list()$HG19$reference$genome,
  germ_resource = build_default_reference_list()$HG19$variant$germ_reference,
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  threads = 4,
  ram = 4,
  mode = "local",
  executor_id = make_unique_id("createPoNGatk"),
  task_name = "createPoNGATK",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

sif_gatk	REQUIRED Path to gatk sif file.
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.
output_name	OPTIONAL Name for the output. If not given the name of one of the samples will be used.
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.
ref_genome	REQUIRED Path to reference genome fasta file.
germ_resource	REQUIREDPath to germline resources vcf file.
verbose	OPTIONAL Enables progress messages. Default False.
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.
normals	OPTIONAL Path to normal BAM file.
pon	OPTIONAL Path to panel of normal.
mnps	OPTIONAL Report MNPs in vcf file.
contamination	OPTIONAL Produce sample cross-contamination reports. Default TRUE.
orientation	OPTIONAL Produce read orientation inforamtion. Default FALSE
filter	OPTIONAL Filter Mutect2. Default TRUE.

Details

For more information about this function: https://gatk.broadinstitute.org/hc/en-us/articles/360037058172-CreateSomaticPanelOfNormals-BETA-

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