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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 that this is an experimental branch. Currently, we need to build a docker image from this repository, but we can't run the reporting.R script from within the container, because it requires access to the REST service above, which will run on localhost port 5000. I haven't figured out yet how to make this accessible from the container, so we run the annotation from the container but create the final report using the plain reporting.R script.

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 install and run the Biograph REST API. Then clone this repository and cd into it.

First, we need to get and run the REST service via docker:

1. git clone https://github.com/mrdivine/clinicalReporting_DB_RESTAPI.git
2. cd clinicalReporting_DB_RESTAPI
3. docker-compose up

Now we clone this repository and checkout the single_script branch:

4. git clone -b single_script https://github.com/PersonalizedOncology/ClinicalReportR.git
5. cd ClinicalReportR
6. docker build -t personalizedoncology/clinicalreportr:latest .
7. export CLINICALREPORTR=`pwd`

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

8. wget http://www.broadinstitute.org/~konradk/loftee/human_ancestor.fa.rz
9. wget http://www.broadinstitute.org/~konradk/loftee/human_ancestor.fa.rz.fai
10. wget https://github.com/Ensembl/VEP_plugins/blob/release/90/LoFtool_scores.txt
11. docker run -t -i -v $CLINICALREPORTR:/home/vep/.vep personalizedoncology/clinicalreportr:latest perl /home/vep/src/ensembl-vep/INSTALL.pl perl INSTALL.pl -a cf -s homo_sapiens -y GRCh38

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

11. docker run -t -i -v $CLINICALREPORTR:/data personalizedoncology/clinicalreportr:latest vep -i /data/strelka.passed.missense.somatic.snvs_test.vcf -o my_annotated.vcf
12. Rscript reporting.R -f my_annotated.vcf

You should now have a file my_annotated.vcf.docx.

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personalizedoncology