shamanpi
commented
4 years ago I'm not sure how many iterations are required, but it would probably go faster if you could split the inbreeding calculations by chromosome (or use a single chromosome if it's heavily inbred). If you want to manually change the iteration thresholds, those can be changed at the bottom of the Inbreeding_Coefficients wrapper script by adding to the ngsF call:
-min_iters [lower_threshold] -max_iters [upper_threshold]
You may have already found this, but ANGSD relies on an underlying ngsF package to do the inbreeding coefficient estimation. They have relevant tutorials and documentation here:
https://github.com/fgvieira/ngsF/tree/master/examples
If, however, you already know your inbreeding coefficients very well and don't want to recalculate them, then the following command will generate a suitable file for angsd-wrapper:
yes [inbreeding_coefficient] | head -n [number_samples] > [project_name].indF
How many iterations does the Inbreeding Coefficient run? I tried reading the documentation but have not found the info. I am running it for a big dataset, it has been running for more than 5 days and is up to iteration 126. I see that its set at max_iters: 1500 min_iters: 10 and in that case it will not be able to finish before running out of time (max 7 days on our server). Is there a way to change this? Does the program need to do all 1500 iterations for the results to be usable?