Use of inversion. During optimisation, a scan is performed in each analysis for inverting the skewness values determining phase downstream of each marker. Based on this scan, knots or bubbles of incorrect phase can be identified and resolved. The two lines are illustrating iteration 2 and 3, respectively, for chromosome 1 in the founder individual with ID 3. In iteration 2, a large range of markers has converged towards an inverted phase versus the correct one. This region is identified and inverted for iteration 3.
Nettelblad BMC Proceedings 2011 5(Suppl 3):S10 doi:10.1186/1753-6561-5-S3-S10