README.md

gpgr - Genomics Platform Group Reporting

Contains reports and functions used in the Genomics Platform Group at the University of Melbourne Centre for Cancer Research.

Conda install

Main modules

PURPLE

Read and process output files from PURPLE - see vignette at https://umccr.github.io/gpgr/articles/purple.html.

HRDetect

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

CHORD

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

MutationalPatterns

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

CLI (v0.2.0)

#------- gpgr -------#
$ inst/src/gpgr.R --help
usage: gpgr [-h] {hrdetect,chord,mutpat} ...

GPG Reporting

positional arguments:
  {hrdetect,chord,mutpat}
                        sub-command help
    hrdetect            hrdetect help
    chord               chord help
    mutpat              mutationalpatterns help

#------- hrdetect -------#
$ inst/src/gpgr.R hrdetect --help
usage: gpgr hrdetect [-h] --sample SAMPLE --snv SNV --sv SV --cnv CNV
                     [--out OUT]

optional arguments:
  --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 -------#
$ inst/src/gpgr.R chord --help
usage: gpgr chord [-h] --sample SAMPLE --snv SNV --sv SV [--out OUT]

optional arguments:
  --sample SAMPLE  Sample name.
  --snv SNV        Input SNV (VCF format).
  --sv SV          Input SV (VCF format).
  --out OUT        Output file ['chord.json.gz']

#------- mutpat -------#
$ inst/src/gpgr.R mutpat --help
usage: gpgr mutpat [-h] --sample SAMPLE --snv SNV --outdir OUTDIR

optional arguments:
  --sample SAMPLE  Sample name.
  --snv SNV        Input SNV file (VCF format).
  --outdir OUTDIR  Output directory to write results to


umccr/gpgr documentation built on Nov. 25, 2021, 1:15 p.m.