diversity_core_collection
Select a core collection maximizing captured allelic diversity via greedy allele-coverage selection. Outputs a ranked list of accessions with cumulative coverage and diversity fraction.
Instructions
Select a core collection that maximises captured allelic diversity.
Greedy allele-coverage selection (Core-Hunter style): repeatedly add the accession
that contributes the most not-yet-captured marker-alleles. Pick the core size
directly, or as fraction of all accessions (default 10%). Writes
core_collection.csv (rank, accession, cumulative allele coverage) and reports the
fraction of total allelic diversity the core captures.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| size | No | Explicit core-collection size (number of accessions); overrides fraction. | |
| 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). | |
| fraction | No | Core-collection size as a fraction of all accessions (default 0.1). | |
| 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
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| result | Yes |