392131 Variation calling challenge (Pj) (WiSe 2012/2013)

Project: Variation calling challenge, 2 ECTS, 4*2 hours

You are given reference genome A and simulated short read data D from genome B. Genome B is
variant of A with some simulated SNPs, and short and large indels. The task is to reconstruct B'
from A and D such that B' is as close to B as possible. The closeness is measured by the alignment
score of B’ and B; the alignment is produced by projecting the alignment of B’ to A, given by
you, to the alignment of B’ to B through the original generated alignment of A to B. You can use
any tools available to produce sequence B’ and its alignment to A.
Dataset is provided by the lecturer. Project lasts 4 weeks and it can be done in small teams.
Guidance is offered 2 hours per week.

Teilnahmevoraussetzungen, notwendige Vorkenntnisse

This class will be given in English.