VarLens

Cohort Analysis ​

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

Cohort view showing aggregated variant data across cases

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.