Post date: Sep 18, 2014 11:22:11 PM
Skipping indel realignment mead a substantial difference on the PCA of LG 1 (uniform prior on genotype) for Moe's data, see pc1to4norealn.pdf vs pc1to4.pdf in /labs/evolution/projects/timema_radiation. I believe that the pattern we now see fits the expectation from the known phylogenetic history of these populations, but I am waiting on Patrik to confirm this. In the mean time, I am continuing with variant calling on all remaining LGs.