autobin_cnvkit: Wrapper around autobin 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 autobin 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

autobin_cnvkit(
  sif_cnvkit = build_default_sif_list()$sif_cnvkit,
  ref_genome = build_default_reference_list()$HG19$reference$genome,
  access = build_default_reference_list()$HG19$reference$access_5k,
  bam = NULL,
  bed = NULL,
  annotation = NULL,
  seq_method = "hybrid",
  split = FALSE,
  short_names = FALSE,
  bp_per_bin = 1e+05,
  min_bin_size_target = 20,
  max_bin_size_target = 20000,
  min_bin_size_antitarget = 500,
  max_bin_size_antitarget = 5e+05,
  ...
)

Arguments

sif_cnvkit	REQUIRED Path to cnvkit sif file.
bed	REQUIRED Path to input BED file with target regions. Default none
annotation	OPTIONAL BED file with region annotation information. Default none
seq_method	OPTIONAL Sequenced methods used. Default hybrid. Options "hybrid","amplicon","wgs"
short_names	OPTIONAL Use short annotation names. Default FALSE
bp_per_bin	OPTIONAL Bases per bin. Default 100000.
min_bin_size_target	OPTIONAL Mininimum target bin size. Default 20.
max_bin_size_target	OPTIONAL Mininimum target bin size. Default 20000.
min_bin_size_antitarget	OPTIONAL Mininimum target bin size. Default 500.
max_bin_size_antitarget	OPTIONAL Mininimum target bin size. Default 500000.
ref_genoma	REQUIRED Path to reference genoms.
bams	REQUIRED Path to BAM files. 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.
seq_type	OPTIONAL Use short annotation names. Default FALSE
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.