Question: Fst value inflation in BayeScan?
gravatar for aesculus
24 months ago by
aesculus10 wrote:

I am testing several RADseq SNP datasets for Fst outliers using BayeScan 2.1. These datasets represent the same sampling of individuals, but with different numbers of SNPs included and either 2 or 3 populations being tested.

I convert .genepop files to the .bayescan file format using PGDSpider. I cannot see any differences among the genepop or bayescan files.

However, when I run BayeScan (using server commandline or GUI on PC), five out of six of my datasets result in Fst values of ~0.5 rather than ~0.01. The latter range seems far more likely, given Fst estimates made in other software such as STACKS and adegenet in R, and because my populations are mostly homogenous, and from a marine organism.

Does anyone have an explanation for why BayeScan is estimating such high Fst values for all but one of my datasets?

fst bayescan fst outlier • 842 views
ADD COMMENTlink modified 23 months ago by Biostar ♦♦ 20 • written 24 months ago by aesculus10

I should also add that BayeScan is also failing to calculate alpha values in the .sel files for the affected datasets.

ADD REPLYlink written 24 months ago by aesculus10
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1214 users visited in the last hour