corrected javadoc for InbreedingCoeff

[davidbenjamin]

Closes #5712.

@ldgauthier can you look at this?

[codecov-io]

Codecov Report

Merging #5768 into master will decrease coverage by 0.001%.
The diff coverage is n/a.

@@               Coverage Diff               @@
##              master     #5768       +/-   ##
===============================================
- Coverage     86.982%   86.981%   -0.001%     
  Complexity     31861     31861               
===============================================
  Files           1943      1943               
  Lines         146770    146770               
  Branches       16223     16223               
===============================================
- Hits          127663    127662        -1     
  Misses         13194     13194               
- Partials        5913      5914        +1

Impacted Files	Coverage Δ	Complexity Δ
...ender/tools/walkers/annotator/InbreedingCoeff.java	86.207% <ø> (ø)	10 <0> (ø)	⬇️
...nder/utils/runtime/StreamingProcessController.java	67.299% <0%> (-0.474%)	33% <0%> (ø)
...itute/hellbender/tools/walkers/mutect/Mutect2.java	84.091% <0%> (ø)	22% <0%> (ø)	⬇️

[ldgauthier]

How can F be a probability when it takes on negative values?

Also, I've never heard of it being called the Fixation Score. Is that in one of your stat gen books?

[davidbenjamin]

How can F be a probability when it takes on negative values?

It's the probability of alleles being IBD provided that inbreeding is the only source of deviation from HWE and in the limit of infinite sample size washing out statistical noise. Under these assumptions it's always positive. How about I rewrite the docs to be much, much clearer about this?

Also, I've never heard of it being called the Fixation Score.

I hadn't heard of it, either, but Wikipedia told me so: https://en.wikipedia.org/wiki/F-statistics

[ldgauthier]

Given that we mostly process human data it might be better to say "consanguinity is the only source of deviation" because inbreeding the context of humans is rather gauche. Sorry for nitpicking. Merge when you're ready.

[davidbenjamin]

Switched to cosanguinuity.

[ldgauthier]

I don't think that's a word: https://www.merriam-webster.com/dictionary/consanguinity

[davidbenjamin]

Oh no!