This repository contains a Snakemake workflow for making clonal hematopoiesis of indeterminate potential (CHIP) calls.
The location of GRCh38 reference and other input files must be configured in config.yml. Mutect2 reference files can be downloaded from gs://gatk-best-practices/somatic-hg38/. A Singularity/Apptainer container image can be built using the definition file chip.def.