I use the Arlequin to caculate the 2D-SFS file. I have a dataset of 2 pops, 52 individuals. But I only got the jointMAFpop1_0.obs file.
BELOW is the arlequin log file: eading Project: Reading input file ... Reading Samples section ... Reading group2 ... done ! (81 ms)
Reading group1 ...
done ! (62 ms)
done reading Samples section! (144 ms)
Reading genetic structure ...
done reading genetic structure! (0 ms)
done ! (144 ms)
Checking all selected options... Building vectors of alleles... done in 18 ms Processing phenotypes into pseudo-haplotypes... done in 1 ms Building vectors of alleles... done in 14 ms done! check selected settings... done!
Population 'group2' : Computing standard diversity indices ... done ! done in 98 ms
Population 'group1' : Computing standard diversity indices ... done ! done in 89 ms
Computing SFS ...
Impossible to compute derived SFS as ancestral allelic state ("0") not found in data.
Consider recoding your data as 0, 1, 2, 3
done ! (1726 ms)
<h6>#</h6>I have noticed the "Impossible to compute derived SFS as ancestral allelic state ("0") not found in data." is it the reason that I can't got the derived SFS? How to code the ancestral allele?
•
written
by
gaojie •
1 answer
Have you solved the problem? can you help me to get unfolded SFS, I need to use the fastsimcoal to do the next work, Thank you very much.
Log in to answer this question.
