estimate_contamination_gatk: Estimate sample contamination Gatk

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

Estimate sample contamination Gatk

Description

This function estimates the sample cross-contamination

Usage

estimate_contamination_gatk(
  sif_gatk = build_default_sif_list()$sif_gatk,
  rdata = NULL,
  selected = NULL,
  tumour = NA,
  normal = NA,
  tumour_pileup = "",
  normal_pileup = "",
  output_name = "",
  output_dir = ".",
  tmp_dir = ".",
  biallelic_db = build_default_reference_list()$HG19$variant$biallelic_reference,
  db_interval = build_default_reference_list()$HG19$variant$biallelic_reference,
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  threads = 1,
  ram = 4,
  mode = "local",
  executor_id = make_unique_id("estimateContaminationGatk"),
  task_name = "estimateContaminationGatk",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

sif_gatk	Path to gatk sif file.
output_name	OPTIONAL Name for the output. If not given the name of one of the samples will be used.
output_dir	Path to the output directory.
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.
f1r2	Path to f1r2 files.
ref_genome	Path to reference genome fasta file.

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