Call CAMDAC for a tumor and patient-matched normal sample

Call CAMDAC for a tumor and patient-matched normal sample

pipeline_tumor_normal(
  patient_id,
  tumor_id,
  normal_id,
  tumor_bam,
  normal_bam,
  sex,
  path,
  pipeline_files,
  build,
  min_tumor = 3,
  min_normal = 10,
  n_cores = 1,
  mq = 0
)

Arguments

patient_id

character. Patient identifier

tumor_id

character. Tumor sample identifier

normal_id

character. Normal sample identifier

tumor_bam

character. Full path to tumor bam file

normal_bam

character. Full path to normal bam file

sex

character. Patient sex: "XX" for female or "XY" for male

path

character. Full path to CAMDAC output directory

pipeline_files

character. Full path to parent directory containing CAMDAC pipeline_files

build

character. Genome build: "hg19" or "hg38"

min_tumor

integer. Minimum read filter for tumor samples

min_normal

integer. Minimum read filter for normal samples

n_cores

integer. Number of cores to use for parallel processing

mq

integer. Minimum mapping quality filter