Code relating to the manuscript "A prospective multicenter study of plasma ctDNA versus archival tumor tissue to guide FGFR-targeted therapy in metastatic urothelial cancer"
All analyses were run on a computational server running the Linux operating system. No non-standard hardware was utilized. Within the PROJECT_DIR, there should be an "alignments" folder with all BAM files.
The project.toml and python_env.yaml files contain dependencies for Julia and Python code, respectively. Additional necessary files are located within the "annotations" folder.
The codebook directory contains all individual scripts to mutations and structural rearrangements. The simple pipeline.sh script can be used to reproduce our results.
Mutato and breakfast can be found here, with instructions to install and process example datasets: https://github.com/annalam/mutato/ and https://github.com/annalam/breakfast respectively. Installizaiton of all tools should take under 1 hour.
Example data and outputs are included in the example_data directory. Extected run time is under 1 hour.