Number of runs to avoid convergence to local maxima

[irbinveliz]

Number of runs to avoid convergence to local maxima

[fgvieira]

Yes, you should always run ngsF several times; how many depends on your data and how much time you can dedicate to it (always changing the seed value, otherwise you get the same results!).

You should do a mixture of approx and full EM, just full EM, using random and estimated initial values (check ngsF.sh); but it all depends how much time it takes and how much time you have.

Then just choose the one with the highest Lkl.

[irbinveliz]

Thank you so much for your quick reply!

My data consist of ultraconserved element data aligned for 80 individuals. I am mainly using ANGSD to calculate different parameters such as SFS and heterozygosity and for that I want to have into account the inbreeding coefficients for each sample.

What is Lkl? Is it the per-individual log-likelihood value from the parameters file? Related to this, how can I read the parameters file? I know it is a binary file but I have not managed to read it properly. I have used the command 'hexdump' but it does not display the file properly.

Another related thing. Is it needed to add the argument --calc_LRT? When I produced the GL for my samples I used the argument -domajorminor.

The commands that I am running are the following:

angsd -gl 1 -doglf 3 -domajorminor 1 -C 50 -minmapq 30 -minQ 20 -baq 1 -uniqueOnly 1 -remove_bads 1 -only_proper_pairs 1 -bam bamlist.txt -out genolike.inbreeding -nThreads 20

ngsF --n_ind 80 --n_sites 1671492 --glf genolike.glf.gz --output filt.inbr.coef

[fgvieira]

Lkl is the final/total log-likelihood.

--calc-LRT is only if you want to test if your inbreeding estimated are different from zero.

[irbinveliz]

Great! Thank you for your time and help!