eagle

Haplotype phasing within a genotyped cohort or using a phased reference panel

Install

All systems
curl cmd.cat/eagle.sh
Debian Debian
apt-get install bio-eagle
Ubuntu
apt-get install bio-eagle
image/svg+xml Kali Linux
apt-get install bio-eagle
Windows (WSL2)
sudo apt-get update sudo apt-get install bio-eagle
Dockerfile
dockerfile.run/eagle

bio-eagle

Haplotype phasing within a genotyped cohort or using a phased reference panel

Eagle estimates haplotype phase either within a genotyped cohort or using a phased reference panel. The basic idea of the Eagle1 algorithm is to harness identity-by-descent among distant relatives—which is pervasive at very large sample sizes but rare among smaller numbers of samples—to rapidly call phase using a fast scoring approach. In contrast, the Eagle2 algorithm analyzes a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods. Please note: The executable was renamed to bio-eagle because of a name clash. Please read more about this in /usr/share/doc/bio-eagle/README.Debian.