Hello everyone,
for my PhD i performed an EHH and an iHS for a certain candidate region (via subsetting all SNPs on that chromosome to 40 SNPs). Now i am curious if i can make a xpEHH inside one population, when inside this population my trait has two characteristics. In practice i have 400 goats and in my population there are animals with long tongues and short tongues. After cLDLA, GWAS and other analysis i was able to narrow down a candidate region (QTL), for my quantitative trait. Now i want to determine with a xpEHH which SNPs are under selection. But does this even make sense, if i consider the animals with short tongue as population 1 and the animals with long tongue as population 2, when they are in the same stall and there is like random meting (because they have the same selective conditions)? Or is a EHH enough in that case. Thanks a lot and nice regards from Germany
