BEAGLE is a state of the art software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. BEAGLE can
- phase genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs, and parent-offspring trios.
- infer sporadic missing genotype data.
- impute ungenotyped markers that have been genotyped in a reference panel.
- perform single marker and haplotypic association analysis.
- detect genetic regions that are homozygous-by-descent in an individual or identical-by-descent in pairs of individuals.
- Linux / Windows / MacOsX
:: MORE INFORMATION
B L Browning and S R Browning (2013)
Improving the accuracy and efficiency of identity by descent detection in population data.
Genetics 194(2):459-71. doi:10.1534/genetics.113.150029
B L Browning and S R Browning (2011)
A fast, powerful method for detecting identity by descent.
The American Journal of Human Genetics 88:173-182.