GBS, coverage and heterozygosity

I’m running some tests on my GBS data to look for population expansion. I know from looking at GBS data from an F1 genetic mapping population that for GBS data heterozygotes can be under called due to variation in amplification and digestions. Also, for my data observed heterozygosity is almost always under expected. Heterozygotes can also be overcalled when duplicated loci are aligned together. The tests I’m going to use explicitly use observed heterozygosity so this is worrying.

Continue reading