VAF Correlation Pipeline

Contact	Organization	Date
patelk26@email.chop.edu (Khushbu Patel)	CHOP	2019-02-21

Summary

This pipeline plots VAF values for various pairs of Samples (Diagnose-Relapse/Diagnose-Diagnose/Relapse-Relapse), label genes of interest and generates plots of total number of mutation across various samples.

Requirements

1. Docker

How to run

• Install docker for Mac (Check your installation by typing docker -h in the terminal and you should see docker help manual open)
• Open docker terminal and execute the following commands

Build a docker image

Save the Dockerfile in a folder (do not rename the Dockerfile file)

docker build -t <image_repository>:<tag> <path/to/Dockerfile>

Running the docker image

docker run -i -t <image_repository>:<tag> /bin/bash

The above command will open an interactive shell, where you will find the resulting files and folders generated by the pipeline. You can navigate through the folders using standard linux commands.

Coping files from Docker container to Host

docker cp <container_Id>:/file/path/within/container /host/path/target

RNA VAF Comparisons

Summary

This script calculates variant allele frequencies for all non-silent VEP passed RNA variants and annotates with its DNA counterpart. The resulting file is a DNA MAF annotated with RNA variants and its corresponding variant allele frequencies.

How to run

Rscript DNA-RNA-VAF.R <DNA_MAF.rda> <RNA_MAF.maf> <clinical_file.txt>