Comments (1)
fgvieira
commented on May 28, 2024
With angsd -doHWE you get an average of per-site inbreeding estimates, while ngsF calculates the average inbreeding across the whole genome. For low coverage samples I'd expect ngsF to be more accurate, but with high coverage both should give similar results.
That said, all your samples have very low inbreeding, so the differences you are seeing might not be relevant. It would be nice to see the differences on a inbred sample.
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Related Issues (20)
- Allow for negative F
- Alow for arbitrary ploidy
- Calculate individual loglkl
- Allow for non-variable sites
- Merge glf.gz from different chromosome HOT 1
- [main] ERROR: wrong number of sites or invalid/corrupt file! HOT 9
- ReferenceID err
- example of angsd --> ngsF ? HOT 1
- cannot read glf HOT 2
- construction of init_values input file HOT 4
- using custom glf instead of angsd output HOT 4
- Suggestions for dealing with batch effects HOT 2
- ngsF leads to unexpected inbreeding estimate of zero HOT 5
- Number of sites in .mafs.gz different from angsd HOT 1
- Supplementary figures 7, 8 and 9 HOT 1
- When should I set --Freq_fixed=TRUE in calculating inbreeding Coefficient? HOT 3
- Problem with gsl during installation HOT 6
- How to enable reading gz output from angsd --glf 3 HOT 4
- Number of runs to avoid convergence to local maxima HOT 4
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