Relatedness Estimator - Tobias Sayre


I am working on Final Project 1: Relatedness Estimator.

About Me

I am a first year biochemistry graduate student.

Goal for end of quarter

The starting goal for this project is to complete the "hard" version of the project:

Measure risk to related siblings given genotypes (ethical issue).
Handle finite sample size of HapMap.
Reconstruct family histories.

Weekly schedule

Week of 5/4/09:

Wiki updated

Week of 5/11/09:

Converged on basic method for calculating likelihood of relatedness.

Week of 5/18/09:

How to calculate the likelihood of relatedness. Use likelihood ratio between probability that two individuals would share the given alleles divided by the probability that two unrelated individuals would share the given alleles.

Week of 5/25/09:

Start coding the basic method, finish figuring out "Medium" solution.

Week of 6/1/09:

Implemented method using Kronecker Deltas to track sharing of alleles between individuals. Relatedness calculated using likelihood ratio.

Problems that came up

What is the best way to incorporate the LD into the calculation?

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