Hi, I built VarGate for my own workflow and I'm sharing it in case it's useful.

I wanted a visual view of post alignement QC metrics with a direct verdict on each patient. MultiQC is great for cross-samples overview but I wanted something that tells me patient by patient whether the T/N pair is usable.

VarGate reads Picard outputs (CollectWgsMetrics, CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics, optionally CollectGcBiasMetrics) and biobambam2 bammarkduplicates2 for one tumor/normal pair and returns an HTML report with visualized metrics and a PASS / WARN / FAIL verdict + a TSV summary.

Thresholds and rules are defined in YAML profiles. The default profile is calibrated for somatic WGS with references adapted to my use case but everything is editable. You can adjust the cutoffs to your context or write your own profile.

The tool fits easily into a snakemake pipeline and the TSV makes it possible to gate the pipeline (skip if FAIL) or feed it back into a MultiQC downstream.

Code : https://github.com/pieetie/vargate