run_hatchet: Preprocess sequencing data

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

Preprocess sequencing data

Description

Preprocess sequencing data

Usage

run_hatchet(
  tumour = NULL,
  normal = NULL,
  chromosomes = NULL,
  env_hatchet = build_default_python_enviroment_list()$env_hatchet,
  config = build_default_hatchet_config(),
  ref_genome = build_default_reference_list()$HG19$reference$genome,
  ...
)

Arguments

tumour	Path to a single or multiple BAM files
normal	Path to a normal matched BAM file
chromosomes	Select chromosomes to analyze. Default NULL
env_hatchet	Hatchet conda enviroment
config	Hatchet configuration for each step

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