RandomCode: What the Package Does (One Line, Title Case)

Description Usage Arguments

View source: R/call_variants.R

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

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

`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.