bin_targets_cnvkit: Create binned target and anitarget beds from target BED file

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

Create binned target and anitarget beds from target BED file

Description

This function wraps around target and antitarget functiosn 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

bin_targets_cnvkit(
  sif_cnvkit = build_default_sif_list()$sif_cnvkit,
  access = build_default_reference_list()$HG19$reference$access_5k,
  bed = NULL,
  annotation = NULL,
  bin_size_antitarget = 1e+05,
  bin_size_target = 100,
  min_bin_size_antitarget = NULL,
  split = FALSE,
  short_names = FALSE,
  ...
)

Arguments

sif_cnvkit	REQUIRED Path to cnvkit sif file.
access	OPTIONAL Path to non-accessible regions to exclude. Default none
bed	REQUIRED Path to input BED file with target regions. Default none
annotation	OPTIONAL BED file with region annotation information. Default none
bin_size_antitarget	OPTIONAL Average bin size for target. Default 500000.
bin_size_target	OPTIONAL Average bin size for target. Default 120.
min_bin_size_antitarget	OPTIONAL Average bin size for target. Default null.
split	OPTIONAL Average bin size for target. Default null.
short_names	OPTIONAL Use short annotation names. Default FALSE
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 Split annotation names.
threads	OPTIONAL Number of threads to split the work. Default 4
ram	OPTIONAL RAM memory to asing to each thread. Default 4
verbose	OPTIONAL Enables progress messages. Default False.
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.