I’m a fan of GEMINI and have been using it for for a year and a half for various exome projects. I have written two scripts that can generate variant summaries from a GEMINI database. I prefer bar plots over the pie charts created by VEP.
I’ve shared the two scripts on GitHub Gist.
wget https://gist.githubusercontent.com/davetang/7874d065ad0f7f268f9b2aba7b06e38b/raw/0f75428c537eb8c514963072c7f1d7af41246d45/plot_gemini.sh wget https://gist.githubusercontent.com/davetang/f1fecbe8c3e683993b0c5cb3f13b4c97/raw/11d061f074bb15fe7a90b1d86f13a575a3767ef4/plot_gemini.R chmod 755 plot_gemini.*
R is used to create the plots and requires three packages: ggplot2, reshape2, and ggthemes. Install the packages if you haven’t already.
my_required <- c('ggplot2', 'reshape2', 'ggthemes') install.packages(my_required)
Now if you run plot_gemini.R, you should get:
plot_gemini.R Error: Please provide input file Execution halted
I’ve put the two scripts in my bin directory, which is in my PATH. Next I just need to change into the directory with my GEMINI database and run plot_gemini.sh. The script expects one *.db file in the directory.
cd /path/to/gemini/database plot_gemini.sh # generates five PDFs ls -1 *.pdf ALL.pdf HIGH.pdf LOW.pdf MED.pdf TYPE.pdf
Refer to the GEMINI documentation for more information on the variant categories (which are based on the Sequence Ontology).
The two scripts are shown below. Basically the script saves the SQL result from GEMINI and uses R to plot the tables. You can easily modify the scripts to create other summary plots.
This work is licensed under a Creative Commons
Attribution 4.0 International License.