call_somatic_sv_manta: Manta wrapper for structural 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 wrapper for structural variant calling

Description

This function wraps the Manta workflow functions for structural variant calling

Usage

call_somatic_sv_manta(
  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_manta = build_default_tool_binary_list()$bin_manta,
  tumour = NULL,
  normal = NULL,
  normal_id = NULL,
  tumour_id = NULL,
  patient_id = NULL,
  regions = NULL,
  ref_genome = build_default_reference_list()$HG19$reference$genome,
  targeted = TRUE,
  annotate = TRUE,
  tabulate = TRUE,
  ...
)

Arguments

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

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