heterozygote excess while simulating SNPs

[aurelle...@gmail.com]

Dear Laurent

I use fsc28 to simulate some SNPs, similar to RADSeq data. I tried the following parameter file, and I launched fsc28 with the -g option:

//Number of population samples (demes)
2
//Population effective sizes (number of genes)
10000
10000
//Sample sizes
60
60
//Growth rates : negative growth implies population expansion
0
0
//Number of migration matrices : 0 implies no migration between demes
0
//historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix
1  historical event
1000 1 0 1 1 0 0
//Number of independent loci [chromosome]
20000 0
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 100 0 0.000000001 0.33

I converted the arp to vcf with PGDSpider for further analyses. Here I don't have so many SNPs, but the point is that I have negative Fis (for example -0.12 here). Where does it come from?

Thanks

Didier