Citation

If you use BEAGLE in a published analysis, please report the BEAGLE version used and cite the appropriate publication or publications listed below.

Expand this section to view citation instructions.

BEAGLE's fastIBD method is described in: - Browning, B. L., & Browning, S. R. (2011). A fast, powerful method for detecting identity by descent. The American Journal of Human Genetics, 88(2), 173–182. https://doi.org/10.1016/j.ajhg.2011.01.010

BEAGLE's methods for detecting homozygosity-by-descent and identity-by-descent are described in: - Browning, S. R., & Browning, B. L. (2010). High-resolution detection of identity by descent in unrelated individuals. The American Journal of Human Genetics, 86(4), 526–539. https://doi.org/10.1016/j.ajhg.2010.02.021

BEAGLE's methods for calling genotypes from genotype likelihood data are described in: - Browning, B. L., & Yu, Z. (2009). Simultaneous genotype calling and haplotype phase inference improves genotype accuracy and reduces false positive associations for genome-wide association studies. The American Journal of Human Genetics, 85(6), 847–861. https://doi.org/10.1016/j.ajhg.2009.11.004

BEAGLE's methods for imputing ungenotyped markers and phasing parent-offspring trios are described in: - Browning, B. L., & Browning, S. R. (2009). A unified approach to genotype imputation and haplotype phase inference for large data sets of trios and unrelated individuals. The American Journal of Human Genetics, 84(2), 210–223. https://doi.org/10.1016/j.ajhg.2009.01.005

BEAGLE's methods for inferring haplotype phase or sporadic missing data in unrelated individuals are described in: - Browning, S. R., & Browning, B. L. (2007). Rapid and accurate haplotype phasing and missing data inference for whole-genome association studies using localized haplotype clustering. The American Journal of Human Genetics, 81(5), 1084–1097. https://doi.org/10.1086/521987

BEAGLE's methods for association testing are described in: - Browning, B. L., & Browning, S. R. (2007). Efficient multilocus association mapping for whole genome association studies using localized haplotype clustering. Genetic Epidemiology, 31(5), 365–375. https://doi.org/10.1002/gepi.20216

BEAGLE's haplotype frequency model was first described in: - Browning, S. R. (2006). Multilocus association mapping using variable-length Markov chains. The American Journal of Human Genetics, 78(6), 903–913. https://doi.org/10.1086/503636