README.md

• 📚 gpgr - Genomics Platform Group Reporting
  • Installation
  • Main modules
    • 🔮 PURPLE
    • sash
  • 🥳 Developers
  • 💻 CLI

📚 gpgr - Genomics Platform Group Reporting

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

• Docs: https://umccr.github.io/gpgr/

Installation

remotes::install_github("umccr/gpgr")

• Or if used inside a conda environment:

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

Main modules

🔮 PURPLE

• Read and process output files from the PURPLE purity/copy number estimator tool from the Hartwig Medical Foundation (https://github.com/hartwigmedical/hmftools/tree/master/purple). See vignette at https://umccr.github.io/gpgr/articles/purple.html.

sash

• Generate a HTML report with results from the sash WGS post-processing workflow
  • https://github.com/scwatts/sash. See the CLI section below for options.

🥳 Developers

See https://umccr.github.io/gpgr/articles/devnotes.html for developer notes.

💻 CLI

A gpgr command line interface is available for convenience.

• If you’re using the conda package, the gpgr.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 gpgr/inst/cli/ directory to your PATH in order to use gpgr.R.

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

gpgr.R --version
gpgr.R 2.1.0

#-----------------------------------#
gpgr.R --help
usage: gpgr.R [-h] [-v] {canrep} ...

UMCCR Genomics Platform Group Reporting

positional arguments:
  {canrep}       sub-command help
    canrep       UMCCR Cancer Report.

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

#-----------------------------------#
#------- Cancer Report -------#
gpgr.R canrep --help
usage: gpgr.R canrep [-h] --af_global AF_GLOBAL --af_keygenes AF_KEYGENES
                     --batch_name BATCH_NAME [--conda_list CONDA_LIST]
                     --img_dir IMG_DIR --key_genes KEY_GENES --oncokb_genes
                     ONCOKB_GENES --somatic_snv_vcf SOMATIC_SNV_VCF
                     --somatic_snv_summary SOMATIC_SNV_SUMMARY
                     --somatic_sv_tsv SOMATIC_SV_TSV --somatic_sv_vcf
                     SOMATIC_SV_VCF --purple_som_gene_cnv PURPLE_SOM_GENE_CNV
                     --purple_som_cnv_ann PURPLE_SOM_CNV_ANN --purple_som_cnv
                     PURPLE_SOM_CNV --purple_purity PURPLE_PURITY --purple_qc
                     PURPLE_QC --purple_som_snv_vcf PURPLE_SOM_SNV_VCF
                     --virusbreakend_tsv VIRUSBREAKEND_TSV --virusbreakend_vcf
                     VIRUSBREAKEND_VCF --dragen_hrd DRAGEN_HRD
                     --bcftools_stats BCFTOOLS_STATS [--out_file OUT_FILE]
                     [--quiet] --result_outdir RESULT_OUTDIR --tumor_name
                     TUMOR_NAME

options:
  -h, --help            show this help message and exit
  --af_global AF_GLOBAL
                        Path to `af_tumor.txt` file.
  --af_keygenes AF_KEYGENES
                        Path to `af_tumor_keygenes.txt` file.
  --batch_name BATCH_NAME
                        Name of batch sample.
  --conda_list CONDA_LIST
                        Path to `conda_pkg_list.txt` file.
  --img_dir IMG_DIR     Path to directory containing PURPLE plots.
  --key_genes KEY_GENES
                        Path to UMCCR cancer gene file.
  --oncokb_genes ONCOKB_GENES
                        Path to OncoKB database file.
  --somatic_snv_vcf SOMATIC_SNV_VCF
                        Path to `somatic-PASS.vcf.gz` SNV VCF.
  --somatic_snv_summary SOMATIC_SNV_SUMMARY
                        Path to `somatic_snv_summary.json` JSON.
  --somatic_sv_tsv SOMATIC_SV_TSV
                        Path to `manta.tsv` TSV file.
  --somatic_sv_vcf SOMATIC_SV_VCF
                        Path to `manta.vcf.gz` VCF file.
  --purple_som_gene_cnv PURPLE_SOM_GENE_CNV
                        Path to `purple.cnv.gene.tsv`.
  --purple_som_cnv_ann PURPLE_SOM_CNV_ANN
                        Path to annotated and prioritised
                        `purple.cnv.somatic.tsv`.
  --purple_som_cnv PURPLE_SOM_CNV
                        Path to `purple.cnv.somatic.tsv`.
  --purple_purity PURPLE_PURITY
                        Path to `purple.purity.tsv`.
  --purple_qc PURPLE_QC
                        Path to `purple.qc`.
  --purple_som_snv_vcf PURPLE_SOM_SNV_VCF
                        Path to `purple.somatic.vcf.gz`.
  --virusbreakend_tsv VIRUSBREAKEND_TSV
                        Path to VIRUSBreakend summary file.
  --virusbreakend_vcf VIRUSBREAKEND_VCF
                        Path to VIRUSBreakend VCF file.
  --dragen_hrd DRAGEN_HRD
                        Path to DRAGEN HRD file
  --bcftools_stats BCFTOOLS_STATS
                        Path to bcftools stats file
  --out_file OUT_FILE   Path to output HTML file (needs '.html' suffix) [def:
                        {tumor_name}_cancer_report.html].
  --quiet               Suppress log printing during rendering.
  --result_outdir RESULT_OUTDIR
                        Path to directory to write tidy JSON/TSV results.
  --tumor_name TUMOR_NAME
                        Name of tumor sample.

#-----------------------------------#