call_variants_strelka_parallel: Call Somatic/Germline variants using Strelka 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 Strelka in parallel This function takes a pair of matched samples or single | multiple germline variants and calls variants on them. To specify the variant calling mode supply the right strelka binary. It is recommended to supply a vcf with indel candidates. This can be generated using MANTA workflow. This function parallelizes the number of jobs that can be run.

Usage

call_variants_strelka_parallel(
  bin_path = "tools/strelka-2.9.10/build/bin/configureStrelkaSomaticWorkflow.py",
  bin_path2 = "tools/manta-1.6.0/build/bin/configManta.py",
  bam_dir = "",
  ref_genome = "",
  output_dir = "",
  patient_id = "",
  germ_pattern = "GL",
  verbose = FALSE,
  targeted = FALSE,
  jobs = 1,
  threads = 3,
  exec_options = "local"
)

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.
patient_id	REQUIRED Patient ID to analyze. Has to be in file names to subselect samples.
germ_pattern	REQUIRED Pattern used to identify germline samples. Ex GL
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
exec_options	OPTIONAL Type of execution. local (Single node) / sge (multiple nodes). Default local.

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