call_refphase: Process ASCAT data using REFPHASE

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

Process ASCAT data using REFPHASE

Description

Process ASCAT data using REFPHASE

Usage

call_refphase(
  bin_allele_counter = build_default_tool_binary_list()$bin_allele_counter,
  ascat_ref = build_default_reference_list(),
  ref_dataset = "battenberg",
  gender = "XY",
  genome_version = "HG19",
  panel_version = "V3",
  tumour = NULL,
  normal = NULL,
  patient_id = NULL,
  homozygous_cutoff = 0.7,
  center_baf = TRUE,
  fit_log2 = TRUE,
  gamma = 1,
  penalty = 25,
  output_dir = ".",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  threads = 8,
  ram = 4,
  mode = "local",
  executor_id = make_unique_id("callRefphase"),
  task_name = "callRefphase",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

ascat_ref	OPTIONAL List with default references.
ref_dataset	OPTIONAL Reference dataset for panel allele and loci selection. Default battenberg
gender	OPTIONAL Sample gender. Default XY.
genome_version	OPTIONAL Genome reference version. Default HG19.
panel_version	OPTIONAL PCF Select panel version. Default V3.
tumour	REQUIRED Path to tumour BAM file/s.
normal	REQUIRED Path to normal BAM file/s.
patient_id	REQUIRED Path to normal BAM file.
homozygous_cutoff	OPTIONAL Cut-off to consider homozygous snps . Default 0.7.
center_baf	OPTIONAL Re-center BAF values. Default TRUE
fit_log2	OPTIONAL Better fit ASCAT log2 ratios. Default TRUE
gamma	OPTIONAL Gamma parameter. Default 1.
penalty	OPTIONAL Penalty parameter. Default 25.
output_dir	OPTIONAL Path to the output directory.
verbose	OPTIONAL Enables progress messages. Default False.
batch_config	OPTIONAL List with default references.
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 "processRefphase"
task_name	Task name. Default "processRefphase"
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.

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