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.
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.
jto save report in JSON format
wto save report in DOCX format
pto save report in PDF format
You should now have the report in ReportApp folder.