diversity_kinship
Computes a genomic relationship matrix from genotyping data to identify related sample pairs and estimate inbreeding levels.
Instructions
VanRaden genomic relationship (kinship) matrix.
Computes G = ZZ'/(2 Σp(1-p)) from alt dosage. Writes the full matrix as
kinship_matrix.csv (samples × samples) and reports the most-related pairs
and the diagonal (self-relationship / inbreeding) range. For large sets pass
method="allelematrix" + max_markers to avoid a full VCF export.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| method | No | Genotype source: 'vcf' (full export, cached) or 'allelematrix' (paged, server-side subset). | vcf |
| region | No | Restrict analysis to a genomic window: 'chrom' or 'chrom:start-end' (1-based). | |
| top_pairs | No | How many most-related sample pairs to report. | |
| output_dir | No | Directory for the output CSV(s) (default ./gigwa_results/<module>/). | |
| max_markers | No | Cap the number of markers analysed (evenly-spaced subsample); omit to use all. | |
| variant_set_db_id | Yes | BrAPI variantSetDbId identifying the run (MODULE§project§run); from list_variant_sets / list_content. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| result | Yes |