Example 4:
For this example we will illustrate analysis of low-coverage sequence data
from a population of individuals.
Like many statistical analyses, the results depend on one's choices for
various thresholds and other parameters.
The parameter values chosen here were validated by comparing these results
with results from higher coverage data for the same individuals.
This example builds a single sequential history, but it is organized
into several parts according to the type of analysis being performed.
These illustrate the following skills.
Part 1:
Population structure.
- Plotting a sequence coverage distribution
- Building a phylogenetic tree using pairwise genetic distances
- Performing principal components analysis
- Grouping individuals
- Characterizing the ancestry of individuals
- Working with composite datasets
Part 2:
Selective sweeps.
- Limiting a dataset to autosomes
- Computing the fixation index
- Detecting selective sweeps