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Last pushed: 3 days 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.


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.

First, we need to get the REST service:

1. git clone

Now we clone this repository and checkout the single_script branch:

2. git clone -b single_script
3. cd ClinicalReportR

Now we download some data for required for ensemble-vep:

4. export CLINICALREPORTR=`pwd`
5. wget
6. wget
7. wget
8. docker run -t -i -v $CLINICALREPORTR:/home/vep/.vep ensemblorg/ensembl-vep perl -a acf -s homo_sapiens -y GRCh37

This will download cache files into $CLINICALREPORTR, e.g. the directory you cloned this repository into.

9. cd ../clinicalReporting_DB_RESTAPI
10. docker-compose build && docker-compose run --service-ports ClinicalReportR -t /data/<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 ClinicalReportR folder.

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