haplotypecaller_gatk: Variant Calling using HaplotypeCaller

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

Variant Calling using HaplotypeCaller

Description

This function functions calls HaplotypeCaller for variant calling. If a vector of normal samples are provided these will be processed in multi-sample mode. To run in normal mode suppply a single normal sample. TO DO// Implement mitochondrial mode feature

Usage

haplotypecaller_gatk(
  rdata = NULL,
  selected = NULL,
  sif_gatk = build_default_sif_list()$sif_gatk,
  normal = "",
  region = "",
  ref_genome = build_default_reference_list()$HG19$reference$genome,
  output_dir = ".",
  tmp_dir = ".",
  output_name = "",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  threads = 4,
  ram = 4,
  mode = "local",
  executor_id = make_unique_id("parallelCallHaplotypecallerGatk"),
  task_name = "parallelCallHaplotypecallerGatk",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

rdata	OPTIONAL Import R data information with list of BAM.
selected	OPTIONAL Select BAM from list.
sif_gatk	REQUIRED Path to gatk sif file.
normal	OPTIONAL Path to normal BAM file.
ref_genome	REQUIRED Path to reference genome fasta file.
output_dir	OPTIONAL Path to the output directory.
tmp_dir	OPTIONAL Path to the temporary directory.
output_name	OPTIONAL Name for the output. If not given the name of the first tumour sample of the samples will be used.
verbose	OPTIONAL Enables progress messages. Default False.
batch_config	REQUIRED Additional batch configuration if batch mode selected.
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.

Details

For more information read: https://gatk.broadinstitute.org/hc/en-us/articles/360037225632-HaplotypeCaller

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