call_sv_svaba: Structural variant calling using svaba

In TearsWillFall/variantCall: An implementation of a wrapper for variant calling using MuTECT2 and Platypus GNU/Unix based systems

Description

This function calls structural variants in a pair of tumor-normal or in single tumor/normal samples matched samples using svaba

Usage

call_sv_svaba(
  tumor_bam = "",
  bin_path = "tools/svaba/bin/svaba",
  bin_path2 = "tools/htslib/bgzip",
  bin_path3 = "tools/htslib/tabix",
  normal_bam = "",
  ref_genome = "",
  threads = 3,
  output_name = "",
  targets = "",
  dbsnp_indels = "",
  verbose = FALSE,
  output_dir = ""
)

Arguments

tumor_bam	REQUIRED Path to tumor bam file.
bin_path	REQUIRED Path to svaba binary executable. Default path tools/svaba/svaba.
bin_path2	REQUIRED Path to bgzip binary executable. Default path tools/htslib/bgzip.
bin_path3	REQUIRED Path to tabix binary executable. Default path tools/htslib/tabix.
normal_bam	OPTIONAL Path to germline bam file.
ref_genome	REQUIRED Path to reference genome fasta file.
threads	OPTIONAL Number of threads to use. Default 3.
output_name	OPTIONAL Name for the output.
targets	OPTIONAL BED file with capture target regions.
dbsnp_indels	OPTIONAL Database with indel annotations.
verbose	OPTIONAL Enables progress messages. Default False.
output_dir	OPTIONAL Path to the output directory.

TearsWillFall/variantCall documentation built on Oct. 15, 2021, 8:51 p.m.