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 the 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
- Working with composite datasets
- Plotting sequence coverage distribution
- Building a phylogenetic tree using pair-wise genetic distances
- Performing principal component analysis
- Grouping individuals
- Estimating the proportions of each individual's ancestry
Part 2:
Detecting selective sweeps
- Filtering to get autosomes
- Computing fixation index
- Finding the selective sweeps