call_sv_manta: Call Somatic/Germline structural variants using Manta This...

Description Usage Arguments

View source: R/analysis.R

Description

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

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
call_sv_manta(
  bin_path = "tools/manta-1.6.0/build/bin/configManta.py",
  tumor_bam = "",
  normal_bam = "",
  ref_genome = "",
  output_dir = "",
  patient_id = "",
  verbose = FALSE,
  targeted = FALSE,
  threads = 3
)

Arguments

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


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