Integrative Variant Analysis
Upload files for multiple variant types (SNPs, INDELs, SVs, etc.) along with shared sample metadata to perform a comprehensive integrative analysis. Follow the steps below to explore your data.
1
Upload & Configure Data
Provide the necessary files for each variant type and select a primary grouping column.Note: At least two different variant types (e.g., SNPs + INDELs) are required for integrative analysis. For single-type analysis, please visit specific pages like SNP Analysis.
1. Select Variant Types to Analyze
Choose which variant types you want to include. You can select multiple types for an integrative analysis.
SNP
Variant Matrix
SNP frequency matrix.
Variant Annotation
Annotation for SNP sites.
INDEL
Variant Matrix
INDEL presence/absence matrix.
Variant Annotation
Annotation for INDEL sites.
2. Upload Sample Metadata
Provide a single metadata file for all samples. This is required to select a grouping column.
Upload metadata first
3. Set Variant Prevalence Thresholds
Define the minimum prevalence (0.0 - 1.0) for a variant to be included in the analysis. Variants appearing in fewer samples than the threshold will be filtered out. (0 = No filtering)
Filter if < 30% samples
Filter if < 10% samples