f2 from qpgraph with NULL as outgroup
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 20/100
Research direction
Begin with the qpgraph output path and the handling of a NULL outgroup; the issue does not name a source file, test, or entry point. Reproduce the reported f2 and Fst comparison, then document whether disabling normalization changes f2 as expected and add a focused regression test if the behavior is confirmed.
Written by the indexing model from the issue text.
Description
Hi All,
I'm wondering what is the scale of f2 in qpgraph output? I set outgroup as NULL to turn off normalization but the resulting f2 seems to be normalized by heterozygosity somewhere. I tried to compute f2 and Fst myself, and my Fst agrees with qpgraph but f2 doens't.
I'm very grateful for the help.
Chi-Chun
- Dominant language
- C
- Stars
- 236
- Forks
- 76
- PR merge metrics
- No merged PRs in 30d
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