GWAS¶

Use GWAS commands to search trait-variant associations from the GWAS Catalog.

Search GWAS¶

By trait:

biomcp search gwas --trait "type 2 diabetes" --limit 10

By gene:

biomcp search gwas -g BRAF

With p-value threshold:

biomcp search gwas -g TCF7L2 --p-value 5e-8 --limit 10

Key flags: -g/--gene for a gene symbol, --trait for phenotype text, and --p-value for a finite significance threshold greater than 0 and at most 1. Exact provider mantissa/exponent values must also represent a probability in that range; BioMCP accepts exponents from -1,000,000 through 0, which preserves extreme underflowed results while rejecting malformed upstream values. Use --limit and --offset for bounded paging. Genomic interval search is not supported by this command.

Get records¶

GWAS is search-only. There is no get gwas subcommand.

Request sections¶

GWAS search rows do not expose extra section names. Use biomcp get variant <id> gwas when you need GWAS evidence attached to a known variant card.

Helper commands¶

GWAS is search-only. Start with search gwas for genes or traits, then pivot into get variant <id> gwas if a specific association needs deeper context.

JSON mode¶

biomcp --json search gwas --trait "type 2 diabetes"

Practical tips¶

Combine gene and trait filters to narrow broad searches.
GWAS data is also available as a variant section: biomcp get variant rs7903146 gwas.