read_extractor_circlemap: Extract Circular Reads using Circlemap tool

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

Extract Circular Reads using Circlemap tool

Description

This function generates a BAM file with circular DNA candidate reads

Usage

read_extractor_circlemap(
  env_circlemap = build_default_python_enviroment_list()$env_circlemap,
  bin_samtools = build_default_tool_binary_list()$bin_samtools,
  bam = NULL,
  ...
)

Arguments

env_circlemap	REQUIRED Conda enviroment for circlemap tool.
bin_samtools	REQUIRED Path to samtools binary file.
bam	OPTIONAL Path to BAM file
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.
sort	Sort BAM file. Default TRUE.
coord_sort	Generate a coord sorted file. Otherwise queryname sorted. Default TRUE
index	Generate an index file for sorted BAM. Default TRUE
clean	Remove input files. Default FALSE
stats	Generate BAM stats. Default all. Options "all","flag","index",""
mode	REQUIRED Where to parallelize. Default local. Options "local","batch"
batch_config	REQUIRED Additional batch configuration if batch mode selected.
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

//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.