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

Description Usage Arguments

View source: R/call_variants.R

Call Somatic/Germline structural variants using Manta This function takes a pair of matched samples or single | multiple germline samples and calls variants on them. Variant calling mode is established based on wheather tumor_bam is supplied or not.

call_sv_manta(
  bin_path = system.file("tools/manta/bin", "configManta.py", package = "RandomCode"),
  tumor_bam = "",
  normal_bam = "",
  ref_genome = "",
  output_dir = "",
  patient_id = "",
  verbose = FALSE,
  targeted = FALSE,
  threads = 3
)

`bin_path`	REQUIRED Path to strelka binary. Somatic or Germline.
`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