[sfscode-users] sample all in the population with --sampSize -1

[Daniel R. <dr...@sa...>]

Hi,

First of all, thanks a lot for writing SFS_CODE and for providing excellent documentation.

I'm attempting to recreate some figures from Zuk et al.'s Searching for missing heritability: Designing rare variant association studies with SFS_CODE. Figures 1 (B) & (C), seen at ( http://www.pnas.org/content/111/4/E455/F1.expansion.html ) are the individual allele frequencies for equillibrium and European populations. I would like to sample the entire population in SFS_CODE to count the allele frequencies and noticed that in the documentation we can do this with the option --sampSize and from Table 6 on p57 of August 15, 2015 it has

Sample <SS1> individuals from population 1, ..., <SSNPOP> individuals from population NPOP. Use the value -1 to sample an entire population. (p??)

I have attempted to grab all samples in the population with the -1 option as follows (note that I am only performing one iteration and using a small population size to for quick testing purposes):

$ sfs_code 1 1 --popSize 1000 --additive --length 1 1500 --substMod 0 --theta 0.034 --selDistType 1 2.91587694999271 0 1 -TE 0 --printGen --sampSize -1 --ploidy 2
> not enough arguments after --sampSize (entry 22)
> For usage type: sfs_code -h<return>

Then I have tried to indicate the population index:
$ sfs_code ... --sampSize 1 -1
> my apologies. -1 has not been implemented.
> For usage type: sfs_code -h<return>

In my example it's not a big deal as the population doesn't grow but in Zuk there is some exponential population growth, which I can approximate if need be - I just wanted to check to see if there was something simple I'm doing wrong.

Cheers,
Dan



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