OCP Tools

Introduction

Set of Oncomine Cancer Panel OCP (renamed as Oncomine Comprehensive Assay (OCA)) and Focus Panel tools to process NCI-MATCH data. This set of tools requires several packages from other repos and sources to be installed.

This set of scripts requires the use of the ir_utils package as well as samtools and other common libraries and programs. More script level requirements listed below with each script.

Current set of scripts and programs available

• collate_moi_reports.py:

  • Concatenate a group of MOI reports generated with match_moi_report.pl for comparison analysis downstream. A bit primitive, but can be helpful for quickie large analyses.

• get_metrics_from_vcf.py:

  • Get some quality metrics from VCF or set of VCFs for reporting. Can report on MAPD, RNA reads, and expression control data.

• match_delinker.py:

  • Script to delink MATCH data for use in other studies.

• match_moi_report.pl:

  • Run rules to generate a report of NCI-MATCH MOIs for a NCI-MATCH VCF file.

• match_positive_control_report.pl:

  • Input one or more VCF files from a MATCH control run and output a report.

• match_rna_qc.pl:

  • New to panel is multi-pooled RNA assays. This script will read the pool level controls to determine how the panel performed as a whole. Requires proprietary panel JSON file that is not for distribution. You can generate this yourself by creating a JSON file starting from the fusions BED file that accompanies each assay panel, and includes the following stucture:

    {
        "ExprControl" : {
            "assay_id" : "pool_number"
        },
        "GeneExpression" : {
            "assay_id" : "pool_number"
        },
        "Fusion" : {
            "assay_id" : "pool_number"
        }
    }
    

• ocp_cnv_report.pl:

  • Generate a CNV report from a VCF file containing IR CNV data. Can filter by gene or CN amplitude. One component of match_moi_report.pl.

• ocp_control_summary.pl:

  • Generate a summary report of the expression control reads in an OCP VCF file. Deprecated and will be replaced fully at some point by the match_rna_qc.pl script.

• ocp_fusion_report.pl:

  • Generate a report of fusions detected in an OCP VCF file. Can show data for whole panel or just positives.

• variant_review.py:

  • Python wrapper script to generate a variant review analysis directory starting with a DNA and an RNA BAM file. This wrapper requires the ir_utils pacakge in order to run.

• dl_reporter.py:

  • Python3 script that relies on the matchbox_api_utils package to add aMOI annotations to a MOI report. This is useful for the so-called Designated Labs effort, where the upfront data is not going to be run through MATCHBox for matching. Right now, relies on match_moi_report.pl (which is why it's a part of this repo), but ultimately should be capable of reading any data.

See the help documentation for each (<program_name> --help) for more detailed information about each.