annotate_bed_circlemap: Annotate Circle-Map circDNA BED file output

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

Annotate Circle-Map circDNA BED file output

Description

This function reads the circle-map circDNA output file

Usage

annotate_bed_circlemap(
  annotation_ref = build_default_reference_list()$HG19$panel$PCF_V3$annotation$genes,
  bed = NULL,
  type = "repeat",
  ...
)

Arguments

annotation_ref	REQUIRED Path to annotation file.
bed	REQUIRED Path to bed file.
type	REQUIRED circleMap output type. Default "repeat".
id	OPTIONAL Sample identifier. If not given the name of the first tumour sample of the samples will be used.
output_dir	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"
hold	OPTIONAL HOld job until job is finished. Job ID.

Details

//TODO validate co-joint calling mode

For more information read: https://github.com/iprada/Circle-Map

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