diversity_fst
Compute pairwise Weir & Cockerham Fst between sample groups to quantify genetic differentiation. Groups defined by JSON or metadata TSV; results saved as CSV.
Instructions
Pairwise Weir & Cockerham Fst between groups of samples.
Define the groups one of two ways:
groups_json— a JSON object mapping each group name to a list of accession names (or callset ids), e.g.{"north": ["112","156"], "south": ["11","42"]}.metadata_tsv+group_column— read groups from a metadata TSV (the same file format used byimport_metadata), keyed onid_column(defaultindividual) and grouped bygroup_column.
Writes fst_pairwise.csv with the Fst for every group pair. (Server-side BrAPI
attributes are not used for grouping — that endpoint is unavailable on the target
Gigwa 2.12 build.)
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). | |
| id_column | No | Column in the metadata TSV holding the individual/accession id (default 'individual'). | individual |
| output_dir | No | Directory for the output CSV(s) (default ./gigwa_results/<module>/). | |
| groups_json | No | JSON object mapping each group name to a list of accession names/ids. | |
| max_markers | No | Cap the number of markers analysed (evenly-spaced subsample); omit to use all. | |
| group_column | No | Column in the metadata TSV holding the group/population label. | |
| metadata_tsv | No | Path to a metadata TSV (import_metadata format) used to define groups. | |
| 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 |