call_variants_strelka: Manta and Strelka wrapper for variant calling

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

Manta and Strelka wrapper for variant calling

Description

This function wraps the functions for variant calling with Strelka and Manta

Usage

call_variants_strelka(
  bin_samtools = build_default_tool_binary_list()$bin_samtools,
  bin_bcftools = build_default_tool_binary_list()$bin_bcftools,
  bin_bgzip = build_default_tool_binary_list()$bin_bgzip,
  bin_tabix = build_default_tool_binary_list()$bin_tabix,
  bin_vep = build_default_tool_binary_list()$bin_vep,
  cache_vep = build_default_cache_list()$cache_vep,
  bin_strelka_somatic = build_default_tool_binary_list()$bin_strelka$somatic,
  bin_strelka_germline = build_default_tool_binary_list()$bin_strelka$germline,
  bin_manta = build_default_tool_binary_list()$bin_manta,
  tumour = NULL,
  normal = NULL,
  patient_id = NULL,
  tumour_id = NULL,
  normal_id = NULL,
  chromosomes = c(1:22, "X", "Y", "MT"),
  regions = NULL,
  ref_genome = build_default_reference_list()$HG19$reference$genome,
  annotate = TRUE,
  tabulate = TRUE,
  targeted = TRUE,
  ...
)

Arguments

bin_strelka_somatic	Path to strelka somatic workflow binary
bin_strelka_germline	Path to strelka germline workflow binary
bin_manta	Path to manta pipeline binary
tumour	OPTIONAL Path to tumour BAM file. If not given will assume germline variant calling.
normal	REQUIRED Path to tumour BAM file.
ref_genome	REQUIRED Path to reference genome FASTA
targeted	REQUIRED Remove coverage filtering for exome/targeted data. Default TRUE
variants	REQUIRED Variants types to call. Default all. Options "snv","sv","all"
indel_cnds	REQUIRED Use indel candidates to correct SNV calls. Default TRUE
output_dir	OPTIONAL Path to the output directory. Default current directory
threads	OPTIONAL Number of threads to split the work. Default 4
batch_config	OPTIONAL Default configuration for job submission in batch.
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"
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.