(2015-May-07, 03:35:54)Chuck Wrote:(2015-May-06, 10:15:17)Duxide Wrote: First of all, the set of 315 Fst values that I calculated using VCFtools (which employs Weir and Cockeram Fst formula) on 1000 Genomes phase 3 data for 26 populations can be seen here (https://docs.google.com/spreadsheets/d/1...sp=sharing ). I report Fst for 1st and 21st chromosomes (columns C and D). They are practically identical (r=0.995) so either can be used to represent the whole genome. Note that these include SNPs and indels. If you use these Fst values in your paper, please cite my last article (http://dx.doi.org/10.6084/m9.figshare.1393160 ) because they are in the supplementary material there.

THERE IS INDEED MUCH CONFUSION ON INTERPRETING FST AS RELATIVE BETWEEN POPULATION VARIANCE.

It appears that the expected BETWEEN population variance should be 2*Fst, after correcting for the inbreeding coefficient.

Davide,

Would it be possible for you to partition global variance into between continental race, between individual within race, and within individual variance?

See table 4 here for an example.

"To measure the differentiation between populations, the widely used statistic FST [17] and its unbiased estimator [18] were used. FST estimates were averaged over all loci, and 95% confidence intervals (CIs) of the average FST were calculated by bootstrap resampling with 10000 replications...Along with FST, variance components were estimated to reflect intra-individual, inter-individual and inter-population differences in genetic variation."

There appear to be programs which allow for this -- but no one does it. If you need, I will write Nishiyama et al. regarding method/statistical program.

Also, link rot: http://dx.doi.org/10.6084/m9.figshare.1393160

Chuck, I ask you to hold for a couple of days. I have worked hard and spent a lot of time trying to get Vcftools to provide variance components (I had to re-write part of the code) and I am almost done, so I'd like you to have a look at those before you publish this paper. Is it ok?