{"enrichment":{"faq":[{"a":"tooluniverse-gwas-finemapping uses Bayesian fine-mapping to compute posterior probabilities for each variant at a GWAS locus, identifying which SNPs are most likely causal rather than just in linkage disequilibrium with the lead variant. The skill generates credible sets\u2014ranked lists of variants with cumulative posterior probability\u2014so you can see the most probable causal candidates and their confidence levels.","q":"Which variant is causal at this GWAS locus?"},{"a":"tooluniverse-gwas-finemapping integrates locus-to-gene (L2G) predictions and eQTL evidence to connect GWAS variants to their target genes. This moves beyond physical proximity, using functional data to show which genes are likely affected by causal variants at a locus, helping distinguish true causal effects from linkage artifacts.","q":"How does tooluniverse-gwas-finemapping link variants to genes?"},{"a":"tooluniverse-gwas-finemapping supports comparison of multiple Bayesian fine-mapping approaches, including methods like SuSiE and FINEMAP. The skill helps you interpret credible sets from different methods, understand their assumptions, and choose the most appropriate approach for your GWAS data and LD structure.","q":"What fine-mapping methods does this skill support?"},{"a":"tooluniverse-gwas-finemapping accounts for linkage disequilibrium (LD) structure to resolve ambiguous causal signals at GWAS loci. By modeling LD patterns, it distinguishes between variants that are truly causal and those merely correlated with the lead SNP, improving the accuracy of credible set construction.","q":"How does tooluniverse-gwas-finemapping handle LD structure?"},{"a":"Yes, tooluniverse-gwas-finemapping annotates variants with functional consequences\u2014such as coding impact, regulatory effects, and conservation scores\u2014to help prioritize causal candidates. Combining posterior probabilities with functional annotations strengthens evidence for which variants are most likely driving disease associations.","q":"Can tooluniverse-gwas-finemapping prioritize variants by function?"},{"a":"A credible set is a ranked list of variants at a GWAS locus ordered by posterior probability of causality. tooluniverse-gwas-finemapping constructs credible sets (typically at 95% confidence) containing the minimum number of variants needed to capture that cumulative probability, helping you focus on the most likely causal SNPs.","q":"What is a credible set in fine-mapping analysis?"}],"shadow_tags":["causal-variant-discovery","bayesian-statistical-methods","ld-block-analysis","credible-set-computation","functional-annotation-tiebreaker","eqtl-gene-linkage","posterior-probability-scoring","multi-signal-detection","population-specific-ld"],"summary_rewrite":"This skill applies Bayesian fine-mapping methods to pinpoint causal variants within GWAS-associated regions, moving beyond the lead SNP to compute posterior probabilities for each variant in a credible set. It integrates locus-to-gene predictions and functional annotations to link variants to their target genes, helping researchers distinguish true causal effects from linkage disequilibrium artifacts."},"files":[{"bytes":10622,"path":"skills/tooluniverse-gwas-finemapping/SKILL.md","sha256":"19e6af5e89b24ac2dbd7574c48f813c2a314093d7cd4fe854d04546f260c2282","url":"https://skillfed.io/files/mims-harvard/ToolUniverse/tooluniverse-gwas-finemapping/6dd2176f/SKILL.md"}],"id":"mims-harvard/ToolUniverse/tooluniverse-gwas-finemapping","links":{"html":"https://skillfed.io/mims-harvard/ToolUniverse/tooluniverse-gwas-finemapping","md":"https://skillfed.io/mims-harvard/ToolUniverse/tooluniverse-gwas-finemapping.md","repo":"https://github.com/mims-harvard/ToolUniverse"},"meta":{"agents_supported":[],"first_seen":"2026-07-28","forks":242,"language":"Python","last_updated":"2026-07-27","license":"Apache-2.0","name":"tooluniverse-gwas-finemapping","publisher":"mims-harvard","stars":1595},"relations":{"similar":[{"id":"mims-harvard/ToolUniverse/tooluniverse-gwas-snp-interpretation"},{"id":"mims-harvard/ToolUniverse/tooluniverse-gwas-trait-to-gene"},{"id":"mims-harvard/ToolUniverse/tooluniverse-variant-to-mechanism"},{"id":"mims-harvard/ToolUniverse/tooluniverse-gwas-drug-discovery"},{"id":"mims-harvard/ToolUniverse/tooluniverse-gwas-study-explorer"},{"id":"mims-harvard/ToolUniverse/tooluniverse-regulatory-variant-analysis"},{"id":"google-deepmind/science-skills/opentargets_database"},{"id":"mims-harvard/ToolUniverse/tooluniverse-pathway-disease-genetics"},{"id":"mims-harvard/ToolUniverse/tooluniverse-population-genetics"},{"id":"mims-harvard/ToolUniverse/tooluniverse-epigenomics-chromatin"}]},"slug":{"owner":"mims-harvard","repo":"ToolUniverse","skill":"tooluniverse-gwas-finemapping"},"version":"6dd2176f"}