Wrappers for somatic mutation signature analysis tools • sigrap

🎶 sigrap

Wrappers for somatic mutation signature analysis tools (HRDetect, CHORD, MutationalPatterns).

Docs: https://umccr.github.io/sigrap/

Installation

remotes::install_github("umccr/sigrap")

Or if used inside a conda environment:

conda install r-sigrap -c umccr -c conda-forge -c bioconda

Main Modules

💻 CLI

A sigrap command line interface is available for convenience.

If you’re using the conda package, the sigrap.R command will already be set up inside an activated conda environment.
If you’re not using the conda package, you need to export the sigrap/inst/cli/ directory to your PATH in order to use sigrap.R.

sigrap_cli=$(Rscript -e 'x = system.file("cli", package = "sigrap"); cat(x, "\n")' | xargs)
export PATH="${sigrap_cli}:${PATH}"

$ sigrap.R --version
sigrap.R 0.1.1

$ sigrap.R --help
usage: sigrap [-h] [-v] {hrdetect,chord,mutpat} ...

Somatic signature wrappers

positional arguments:
  {hrdetect,chord,mutpat}
                        sub-command help
    hrdetect            HRDetect help
    chord               CHORD help
    mutpat              MutationalPatterns help

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit



#------- HRDetect -------#


$ sigrap.R hrdetect --help
usage: sigrap hrdetect [-h] --sample SAMPLE --snv SNV --sv SV --cnv CNV
                       [--out OUT]

optional arguments:
  -h, --help       show this help message and exit
  --sample SAMPLE  Sample name.
  --snv SNV        Input SNV (VCF format).
  --sv SV          Input SV (VCF format).
  --cnv CNV        Input CNV (TSV format).
  --out OUT        Output file ['hrdetect.json.gz'].



#------- CHORD -------#


$ sigrap.R chord --help
usage: sigrap chord [-h] --sample SAMPLE --snv SNV --sv SV [--out OUT]

optional arguments:
  -h, --help       show this help message and exit
  --sample SAMPLE  Sample name.
  --snv SNV        Input SNV (VCF format).
  --sv SV          Input SV (VCF format).
  --out OUT        Output file ['./chord.json.gz']



#------- MutationalPatterns -------#


$ sigrap.R mutpat --help
usage: sigrap mutpat [-h] --sample SAMPLE --snv SNV --outdir OUTDIR

optional arguments:
  -h, --help       show this help message and exit
  --sample SAMPLE  Sample name.
  --snv SNV        Input SNV file (VCF format).
  --outdir OUTDIR  Output directory to write results to.

🎶 sigrap

Installation

Main Modules

🔍 HRDetect

🎸 CHORD

🐾 MutationalPatterns

💻 CLI