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 https://github.com/mrdivine/clinicalReporting_DB_RESTAPI.git
Now we clone this repository and checkout the single_script branch:
2. git clone -b single_script https://github.com/PersonalizedOncology/ClinicalReportR.git 3. cd ClinicalReportR
Now we download some data for required for ensemble-vep:
4. export CLINICALREPORTR=`pwd` 5. wget http://www.broadinstitute.org/~konradk/loftee/human_ancestor.fa.rz 6. wget http://www.broadinstitute.org/~konradk/loftee/human_ancestor.fa.rz.fai 7. wget https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/90/LoFtool_scores.txt 8. docker run -t -i -v $CLINICALREPORTR:/home/vep/.vep ensemblorg/ensembl-vep perl INSTALL.pl -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.
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 ClinicalReportR folder.