call_sv_manta_parallel: Call Somatic/Germline variants using MANTA in parallel This...

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

Description

Call Somatic/Germline variants using MANTA in parallel This function takes a pair of matched samples or single | multiple germline variants and calls variants on them. This function parallelizes the number of jobs that can be run at single time.

Usage

call_sv_manta_parallel(
  bin_path = "tools/manta-1.6.0/build/bin/configManta.py",
  bam_dir = "",
  ref_genome = "",
  output_dir = "",
  verbose = FALSE,
  targeted = FALSE,
  jobs = 1,
  threads = 3
)

Arguments

bin_path	REQUIRED Path to strelka binary. Somatic or Germline.
bam_dir	REQUIRED Path to directory with BAM files.
ref_genome	REQUIRED Path to reference genome.
output_dir	OPTIONAL Path to the output directory.
verbose	DEFAULT==FALSE Enables progress messages.
targeted	OPTIONAL If exome/capture method. Default FALSE
jobs	OPTIONAL Number of jobs. Default 1
threads	OPTIONAL Number of threads per job. Default 3

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