What is war_cat?

WAR_CAT is a script that automates running a genetics analysis tool called PharmCAT, which produces a pharmacogenomic report, meaning a report about how a person's genetic makeup might affect how they respond to certain medications. It takes raw genomic sequencing files, such as VCF or gVCF files and optionally BAM files, and turns them into a finished PharmCAT report without requiring the user to run each step of the pipeline by hand. A notable design choice is that it runs PharmCAT using plain Java rather than Docker, specifically to avoid Docker Hub network failures that can happen when pulling container images. It installs PharmCAT by downloading a specific pinned version directly from GitHub instead. The pipeline detects the input files, figures out whether they are gVCF or plain VCF format and checks the chromosome naming convention used, downloads a matching reference genome, builds a working VCF file by either re-calling from a BAM file or expanding the gVCF, and removes a particular data field that would otherwise cause the normalization step to crash. If a BAM file is present, it also calls a specific gene called CYP2D6 using a tool named Aldy. It then runs PharmCAT's own preprocessing step and finally generates an HTML report. Running it requires Java 17 or newer along with several genomics command line tools, and on Windows the whole process is meant to run inside WSL rather than through Docker Desktop. The first run downloads PharmCAT itself along with two reference genome files, each around 0.9 gigabytes, but these are cached so later runs are much faster. Several environment variables let you override details like which PharmCAT version to use or force a specific CYP2D6 result. The README explicitly states this is not a clinical tool and that anything important produced by the report should be confirmed before being acted on. It also notes the pipeline has been verified against genomic data from sequencing.com and that patches may still be needed.