Analysis of population genetic data often includes the search for
genomic re- gions with signs of recent positive selection. One of the
approaches involves the concept of Extended Haplotype Homozygosity and
its associated statistics. These statistics presume that haplotypes are
phased and some of them that variants are polarized. Here we assess the
consequences if one of the two con- ditions is not fulfilled. We find
that phasing information is indispensable for the accurate estimation of
within-population statistics and, if sample sizes are small, for
cross-population statistics, too. Ancestry information, in contrast, is
of lesser importance for both. We make use of a publicly available
update of our R package rehh which, among other features, incorporates
the adapted statistics presented here.