pileup_summary_gatk: Generate a pileup summary for BAM file

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

Generate a pileup summary for BAM file

Description

This function generates a pilelup summary for a bam file

Usage

pileup_summary_gatk(
  sif_gatk = build_default_sif_list()$sif_gatk,
  bam = "",
  output_name = "",
  output_dir = ".",
  rdata = NULL,
  selected = NULL,
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  biallelic_db = build_default_reference_list()$HG19$variant$biallelic_reference,
  db_interval = build_default_reference_list()$HG19$variant$biallelic_reference,
  threads = 1,
  ram = 4,
  mode = "local",
  executor_id = make_unique_id("pileupSummaryGatk"),
  task_name = "pileupSummaryGatk",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

sif_gatk	Path to gatk sif file.
bam	Path to a BAM file
output_name	OPTIONAL Name for the output. If not given the name of one of the samples will be used.
output_dir	Path to the output directory.
verbose	OPTIONAL Enables progress messages. Default False.
threads	OPTIONAL Number of threads to split the work. Default 4
ram	OPTIONAL RAM memory to asing to each thread. Default 4
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.

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