reference_cnvkit: Wrapper around reference function from CNVkit

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 reference function from CNVkit

Description

This function wraps around target function for CNVkit This function generates an target BED file from an input target file. Additional parameters can be used to exclude regions and modify the average bin size

Usage

reference_cnvkit(
  sif_cnvkit = build_default_sif_list()$sif_cnvkit,
  ref_genome = build_default_reference_list()$HG19$reference$genome,
  cnn = NULL,
  gender = "male",
  gc = TRUE,
  edge = TRUE,
  rmask = TRUE,
  verbose = FALSE,
  cluster = FALSE,
  min_cluster_size = 10,
  male_reference = FALSE,
  threads = 1,
  ram = 1,
  ...
)

Arguments

sif_cnvkit	REQUIRED Path to cnvkit sif file.
cnn	REQUIRED Path to normal coverage profiles. Default none
gender	OPTIONAL Sample gender. Default male.
gc	OPTIONAL Disble GC bias correction. Default FALSE.
edge	OPTIONAL Disble edge correction. Default FALSE.
rmask	OPTIONAL Disble repeat mask correction. Default FALSE.
verbose	OPTIONAL Enables progress messages. Default False.
cluster	OPTIONAL Calculate and store summary stats for clustered subsets of the normal samples with similar coverage profiles. Default FALSE
min_cluster_size	OPTIONAL Minimum size to keep in reference profiles.
male_reference	OPTIONAL Adjust X chromosome to log2 0. Default FALSE.
threads	OPTIONAL Number of threads to split the work. Default 4
ram	OPTIONAL RAM memory to asing to each thread. Default 4
ref_genoma	REQUIRED Path to reference genoms.
target	OPTIONAL Path to BED file with target regions. Default none.
antitarget	OPTIONAL Path to BED file with target regions. Default none.
output_name	OPTIONAL Name for the output. If not given the name of the first tumour sample of the samples will be used.
output_dir	OPTIONAL Path to the output directory.
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 read: https://cnvkit.readthedocs.io/en/stable/pipeline.html

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