call_variants_strelka: Call Somatic/Germline single nucleotide variants using...

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

Description

Call Somatic/Germline single nucleotide variants using Strelka 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

Usage

call_variants_strelka(
  bin_path = "tools/strelka-2.9.10/build/bin/configureStrelkaSomaticWorkflow.py",
  bin_path2 = "tools/manta-1.6.0/build/bin/configManta.py",
  bin_path3 = "tools/bcftools/bcftools",
  bin_path4 = "tools/htslib/bgzip",
  bin_path5 = "tools/htslib/tabix",
  tumor_bam = "",
  normal_bam = "",
  ref_genome = "",
  output_dir = "",
  patient_id = "",
  verbose = FALSE,
  targeted = FALSE,
  threads = 3,
  exec_options = "local"
)

Arguments

bin_path	REQUIRED Path to strelka binary. Somatic or Germline.
bin_path2	REQUIRED Path to manta binary. Somatic or Germline.
bin_path3	REQUIRED Path to bcftools binary.
bin_path4	REQUIRED Path to bgzip binary.
bin_path5	REQUIRED Path to tabix binary.
tumor_bam	REQUIRED Path to tumor bam file.
normal_bam	OPTIONAL Path to normal samples bam files.
ref_genome	REQUIRED Path to reference genome.
output_dir	OPTIONAL Path to the output directory.
patient_id	OPTIONAL Patient ID to name files after. If not given tumor_bam file name will be used, and if this is not given then normal_bam file will be used.
verbose	DEFAULT==FALSE Enables progress messages.
targeted	OPTIONAL If exome/capture method. Default FALSE
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.