create_genomic_db_gatk: Wrapper around CreateDBImport 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 CreateDBImport from GATK package

Description

This function creates a genomic database

Usage

create_genomic_db_gatk(
  sif_gatk = build_default_sif_list()$sif_gatk,
  bin_samtools = build_default_tool_binary_list()$bin_samtools,
  bin_bgzip = build_default_tool_binary_list()$bin_bgzip,
  bin_tabix = build_default_tool_binary_list()$bin_tabix,
  vcfs = "",
  regions = NULL,
  output_dir = ".",
  ref_genome = build_default_reference_list()$HG19$reference$genome,
  verbose = FALSE,
  size = 10,
  batch_config = build_default_preprocess_config(),
  threads = 4,
  ram = 4,
  mode = "local",
  executor_id = make_unique_id("createGenomicDB"),
  task_name = "createGenomicDB",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

sif_gatk	REQUIRED Path to gatk sif file.
vcfs	OPTIONAL Path to VCFs files. Only required if BAM files are not given.
output_dir	OPTIONAL Path to the output directory.
ref_genome	REQUIRED Path to reference genome fasta file.
verbose	OPTIONAL Enables progress messages. Default False.
size	OPTIONAL Number of VCF per thread. Default 10.
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.

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.