construction of init_values input file

[DrLaurenCWhite]

Hi Felipe,
I was wondering if you could tell me how to construct the input file for --init_values?
I would like to use --fixed_freq and a list of MAF values that I previously estimated from a subset of my data. The total dataset contains a lot of close relatives which I think would skew the MAF estimates.
Thanks a lot,
-Lauren

[fgvieira]

Hi Lauren,

the format of the input file for --init_values is the same as the output .pars file, namely a binary file with:

• global log-likelihood (1 double)
• per-individual log-likelihood (N_IND doubles)
• per-individual inbreeding coefficients (N_IND doubles)
• minor allele frequencies (N_SITES doubles)

since you are only interested on the MAF, you can just include dummy values for the other parameters (lkl and inbreeding).
Hope it makes sense. 😄

[DrLaurenCWhite]

Thanks for your quick response!
Just to be clear, the file then contains just 4 lines?
Thanks again!

[fgvieira]

The file is binary, so there are no 'real' lines... but if you have 10 individuals and 1000 sites, your file will have 1021 doubles (1 + 10 + 10 + 1000)

[DrLaurenCWhite]

ah I see! Great, thanks again.