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Last pushed: 2 months ago
Short Description
Create clinical reports in docx format from vcf files
Full Description

Clinical Reporting in R

This is a prototype implementation of a clinical reporting pipeline in R.
Currently, it creates a genetic report of somatic mutations from a vcf file annotated via Ensembl Variant Effect Predictor.

Note: CIvic only supports reference genome build 37.

Usage

We assume that we want to create a report for a vcf file my.vcf residing in $HOME, and that you have R and Docker installed. First, follow instructions to download the Biograph REST API.

We clone this repository and checkout the single_script branch:

1. git clone -b single_script https://github.com/PersonalizedOncology/ClinicalReportR.git

Pelase note that the input VCF file should be in ReportApp folder.

2. cd ClinicalReportR/
3. docker-compose run --service-ports ClinicalReportR -t /inout/<VCF FILE> -p jwp

  • -t: input file name. This should be in the data volume of ClinicalReportR service.
  • -p: output format to save the results.
    • j to save report in JSON format
    • w to save report in DOCX format
    • p to save report in PDF format

You should now have the report in ReportApp folder.

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personalizedoncology