eggd_plot_variant_baf

What does this app do?

Plots BAF and depth of variants from given VCF

What data are required for this app to run?

Required input files:

1. A VCF file (.vcf) - containing the merged small variants we want to plot.
2. R packages (.tar.gz) - compressed tarball of R packages needed to generate plot.

R Packages and Versions:

• stringr (v1.5.1)
• dplyr (v1.1.4)
• karyoploteR (v1.28.0)
• polars (v0.22.0)

How to build the package The package was built on Ubuntu 24.04 and R v4.3. Below are the steps:

1. Update and install the required dependencies:

sudo apt-get update
sudo apt-get install -y libssl-dev libxml2-dev gcc pkg-config

2. Run the R script to install the required R packages:

Rscript scripts/packages.R

3. Compress the R library folder:

tar -czvf R_packages.tar.gz R/library

What does this app output?

This app outputs:

• {prefix}.png : Image of the generated plot in PNG format.

How to run this app from command line?

dx run eggd_plot_variant_baf \
-ivcf=file-xxxx \
-ipackages=file-xxxx  \
--destination="output/eggd_plot_variant_baf"

Notes

The current version of the plotting has the following constraints:

• plotting of variant depth is currently hard limited at DP<50, has a upper Y axis limit of 750 and plots the mean depth across 1000 consecutive variants
• plotting of the BAF is hard limited at < 0.04 and > 0.96