BatchQC

BatchQC is a web app (with optional desktop agent) that monitors genomics pipelines for batch effects and sample swaps across runs, lanes, and sites. It ingests standard outputs (FASTQC/MultiQC summaries, alignment metrics, VCF stats, coverage reports) and flags anomalies like sudden GC bias shifts, contamination spikes, sex discordance, unexpected relatedness, and plate-position artifacts. The MVP focuses on pragmatic, explainable alerts rather than fancy dashboards: what changed, when, likely cause, and the minimum set of checks to confirm. It supports templated QC policies per assay (WGS/WES/RNA-seq/panels) and produces audit-friendly PDF/JSON reports for CLIA/CAP documentation. This is a combination traditional + AI app: traditional rules and thresholds for reliability, plus lightweight ML for drift detection and outlier scoring. It’s not a LIMS replacement; it’s a QC “tripwire” that sits beside existing pipelines.