ExomeFlow

ExomeFlow is a Python package that provides a complete, automated Whole Exome Sequencing (WES) analysis workflow from raw FASTQ files to functionally annotated variants in a single reproducible CLI command. It aims to be the standard high-level pipeline for WES analysis in Python, combining GATK best-practice variant calling, hard filtering, and ANNOVAR annotation into one modular, maintainable package. It handles cohort-level processing (multiple samples), checkpointing for resumable runs, structured logging, and parallel execution out of the box.