Inferring shared chromosomal segments with Germline

The discovery of shared chromosomal segments among individuals can have many applications: finding relationships across individuals, estimating strong bottlenecks, or possible signals of selection.

To execute this recipe, we will use Germline, which is an efficient tool for performing the inference of shared chromosomal segments. It requires phased data. Phased data allows you to assign genotyped data to a specific chromosome, that is, instead of having a list of genotype calls per position, we end up with reconstructed haplotypes.

Getting ready

The preparation of data requires some work. First, we must provide the final phased haplotypes for our dataset in the notebook directory so that you can skip the following process, save for the trivial download of integrated_call_samples.20101123.ped. The directory from the repository is Chapter10. The Notebook is Germline.ipynb, the data file is good.match.gz, and the code support files are merge...