Core hunter in binary SNP data

[eating kuo]

I have used Corehunter for my SNP dataset,The SNP frequency table is binary,so the frequence types are 0,0.5,1.

When I use core.analyser.run for criteria validation,the Heterozygous loci become 0.3~0.4,but in the SNP dataset,the heterozygous loci is less than 0.01.

Is there any problem in Corehunter?

[Herman De Beukelaer]

Hi,

What Core Hunter and Core Analyzer calculate as HE is the expected proportion of heterozygous loci in offspring produced through random mating within a set. The highest value is attained when both alleles of each marker occur with the same frequency in the population. Even if all individuals in your dataset are fully homozygous the set or a subset can have a high HE value, meaning that there is a lot of diversity in that set. It does not mean that there are a lot of heterozygous loci but that a lot are expected to be produced in the offspring.

Best regards,

Herman

Op woensdag 23 maart 2016 20:09:48 UTC+1 schreef eating kuo: