Is There An Alternantive To The Fixation Index To Select Snps Which Are Under Pos. Selection Pressure?

Question

[munch]

In a set of SNPs from different human populations I want to identify those SNPs in genes which are under positive selection pressure. Is there a other / better way or is the bet aproach to calculate the FST Value for each SNP and selecting only those with a high FST value ?

The fixation index is a measure of how populations differ genetically. One derivation of the fixation index is FST = (HT – HS)/HT, in which HT and HS represent heterozygosity of the total population and of the subpopulation, respectively. This derivation measures the extent of genetic differentiation among subpopulations. The value of FST can theoretically range from 0.0 (no differentiation) to 1.0 (complete differentiation, in which subpopulations are fixed for different alleles).

taken from http://www.nature.com/scitable/topicpage/using-snp-data-to-examine-human-phenotypic-706

Thanks

Answer 1

[Zev.Kronenberg]

iHS, XP-EHH, CMS, Haplotype Test, Chi-SQ, liklihood ratio test and population branch statistic are all test that can be used to identify SNPs under selection.

The question is what type of selection are you looking for?