• 🎶 sigrap
  • Installation
  • Main Modules
    • 🔍 HRDetect
    • 🎸 CHORD
    • 🐾 MutationalPatterns
  • 💻 CLI

🎶 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

🔍 HRDetect

Wraps functionality from the HRDetect framework - see vignette at https://umccr.github.io/sigrap/articles/hrdetect.html.

🎸 CHORD

Wraps functionality from CHORD - see vignette at https://umccr.github.io/sigrap/articles/chord.html.

🐾 MutationalPatterns

Wraps functionality from MutationalPatterns - see vignette at https://umccr.github.io/sigrap/articles/mutationalpatterns.html.

💻 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.