access_cnvkit: Wrapper around access command in 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 access command in CNVkit

Description

Create a BED file with non-mappable regions to exclude from the genome. Additional regions can be supplied in a BED format using the exclude_regions argument

Usage

access_cnvkit(
  sif_cnvkit = build_default_sif_list()$sif_cnvkit,
  ref_genome = build_default_reference_list()$HG19$reference$genome,
  exclude_regions = NULL,
  gap_size = 5000,
  ...
)

Arguments

sif_cnvkit	REQUIRED Path to cnvkit sif file.
ref_genome	REQUIRED Path to reference genome fasta file.
exclude_regions	REQUIRED Additional regions to exclude in BED format. 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.
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.