call_sv_svaba_parallel: Structural variant calling using svaba in parallel

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 matched samples pairs using svaba in parallel

Usage

call_sv_svaba_parallel(
  bin_path = "tools/svaba/bin/svaba",
  targets = "",
  bam_dir = "",
  patient_id = "",
  germ_pattern = "GL",
  ref_genome = "",
  jobs = 3,
  threads = 1,
  par_type = "Joint",
  verbose = FALSE,
  output_dir = ""
)

Arguments

bin_path	REQUIRED Path to svaba binary executable. Default path tools/svaba/svaba.
targets	OPTIONAL BED file with capture target regions.
bam_dir	REQUIRED Path to bam files.
patient_id	REQUIRED Patient ID patter to filter samples with.
germ_pattern	OPTIONAL Patient ID pattern to filter samples with.
ref_genome	REQUIRED Germline pattern to filter samples with
jobs	OPTIONAL Number of paired jobs to run. Only when par_type is Paired. Default 3.
threads	OPTIONAL Number of threads to use per job. Default 1.
par_type	OPTIONAL Parallelization type. Joint: Runs a single job with multiple samples jointly | Paired: Runs a pair of tumor-normal through multiple jobs.
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.