Cohort Analysis

VarLens supports aggregating variants across multiple cases for cohort-level analysis.

Switching to Cohort Mode

Use the mode toggle in the toolbar to switch between Case and Cohort views. Cohort mode aggregates all imported cases into a single table view.

Cohort Table

The cohort table shows:

• Carrier count — Number of cases carrying each variant
• Homozygous count — Cases with homozygous genotype
• Affected carriers — Carriers with affected status
• All standard variant columns (gene, consequence, scores, etc.)

Gene Burden Analysis

VarLens includes gene burden testing to identify genes with statistically significant variant enrichment:

• Fisher's exact test — p-value, odds ratio, and 95% confidence interval
• Logistic burden test — p-value and beta coefficient
• FDR-adjusted q-values for multiple testing correction
• Volcano plot and Manhattan plot visualizations of results

Filtering

Cohort view supports the same filtering capabilities as case view, plus additional cohort-specific filters for carrier count thresholds.