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Question: bayenv2: "initial epsilon zero or 1 locus 6912"
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gravatar for biosol
20 months ago by
biosol • 150
biosol • 150 wrote:

Hi everyone,

currently I'm running bayenv2 on my data. First,I've converted my vcffile into bayenvformat but then, when I try to generate the covariance matrix, I get the message initial epsilon zero or 1 locus 6912. I've read that the epsilon value in bayenv2is related to the allele frequency at a specific locus for the current generation, but don't actually understand what this means and I don't know how to solve this problem.

Any help will be appreciated! Thank you very much in advanced :)
bayenv2 snps • 539 views
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modified 19 months ago by katuckele • 10 • written 20 months ago by biosol • 150
1
gravatar for katuckele
19 months ago by
katuckele • 10
katuckele • 10 wrote:

Hi Sonia,

I had this error message too. I checked my SNP file and sure enough, the locus referenced by the error message was fixed in all populations, e.g.:

0 0 0 0 0 0

20 20 20 20 20 20

I took out this locus and Bayenv runs without error.

Hope this helps, Katie
ADD COMMENT • link modified 19 months ago • written 19 months ago by katuckele • 10

Hi Katie, thank you very much for your answer! I asked the developpers of the bayenv2 and they told me that the problem was that the file contained SNPs with fixed allele frequencies (the same allele in all individuals, either 0 or 1). So I filtered my data by MAF 1% and the problems was solved. I think this matches as well with your case, your allele freqs were fixed for that SNP!

ADD REPLY • link written 19 months ago by biosol • 150
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