Comments (1)
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
from angsd-wrapper.
Related Issues (10)
- Error when setup dependencies HOT 8
- compilation error (abcHWE.cpp:272:8: error: βisnanβ was not declared in this scope) HOT 2
- [Problem opening file: '-fold'] --> angst-wrapper SFS ./Site_Frequency_Spectrum_Config in online tutorial HOT 4
- .clst files for shiny graphing for PCA plots
- Fst wrapper - graphing issue HOT 3
- Issue with shiny graphing (running ./angsd-wrapper) HOT 1
- issue running shiny graphing HOT 2
- Adding more filters than are in the Common_config HOT 2
- Install issue;gsl HOT 1
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from angsd-wrapper.