BFMAP by Jicai Jiang

Bayesian Fine-Mapping and Association for Population and Pedigree Data

BFMAP is a C++ program for genetic fine-mapping and SNP-set association of quantitative traits. It handles phenotypes and genotypes from samples with population structure and/or relatedness.

Key features:

• SNP-heritability estimation
• Genome-wide single-marker and SNP-set association analysis
• Fine-mapping via forward selection or shotgun stochastic search

Companion R package: GEMRICH integrates BFMAP results with functional annotations:

• Estimating genetic effect enrichment in functional annotations
• Incorporating functional enrichment into fine-mapping

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Manual

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Download

The executable file is released under the MIT lincense.

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Example Data

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Questions and Help Requests

If you have any questions or bug reports, feel free to email Jicai Jiang at jicai_jiang@ncsu.edu.

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Citation

Fine-mapping with forward selection

Jiang J, Cole JB, Freebern E, Da Y, VanRaden PM, Ma L. Functional annotation and Bayesian fine-mapping reveals candidate genes for important agronomic traits in Holstein bulls. Commun Biol. 2019 Jun 18;2:212. doi: 10.1038/s42003-019-0454-y. PMID: 31240250; PMCID: PMC6582147.

Fine-mapping with shotgun stochastic search

Wang J, Tiezzi F, Huang Y, See G, Schwab C, Wei J, Maltecca C, Jiang J. Fine-mapping methods for complex traits: essential adaptations for samples of related individuals. Brief Bioinform. 2025 Nov 1;26(6):bbaf614. doi: 10.1093/bib/bbaf614. PMID: 41269279; PMCID: PMC12636493.