/dnacopy-tool

Primary LanguageRApache License 2.0Apache-2.0

snp6cbs: Segment TCGA SNP6 tangent normalized data

  • Version: 2.1
  • Authors: Zhenyu Zhang (zhenyuz.cdis@gmail.com)
  • Description: The package converts TCGA SNP6 tangent normalized data (produced previously by TCGA using BirdSuite package) into copy number segmentation files
  • License: Apache 2.0

Dependencies:

  • R (>= 3.2.0)
  • tools
  • parallel
  • data.table (>= 1.9.6)
  • DNAcopy (>= 1.44.0)
  • futile.logger (>= 1.4.3)
  • optparser (>= 1.4.4)

Metadata Requirement

Probeset_Description File: a six column TSV file containing the following information

  • probeid: SNP6 probeset ID
  • chr: chromosome
  • pos: coordinate of the center of probe
  • strand: strand
  • type: SNP6 or CN proble
  • freqcnv: probe in frequent copy number variation regions in germline (boolean)
  • par: probe in Pseudo-Autosomal Regions (PAR) (boolean)

Two example probe description files in GRCh38 are provided in ./meta folder.

  • snp6.na35.liftover.hg38.txt.gz is generated from coordinate liftover (default for command-line mode)
  • snp6.na35.remap.hg38.subset.txt.gz is generated from probe sequence remap (recommended)

Usage

Two modes of running are supported In command-line running mode, the script SNP6CBS.r process one input file each time

Rscript SNP6CBS.r --file=tangent_normlized_file --out1=output_allcnv_file --out2=output_nocnv_file --meta=probeset_description_file --gender=gender --sample=sample_id --log=output_log_file

In parallel mode, SNP6CBS.paralle.r will build a parallel cluster to process each sample. This mode requires a job description file, whose file name is hardcoded in the script as

job_file = "../cbs.jobs.20180214.txt"

A sample job file is provided in ./example/cbs.jobs.20180214.txt. Please check file header for descriptions of each field.