<p>I checked inbreeding coefficient (F) on my samples (around 200)  using plink </p>

<pre><code>plink --file mydata --het
</code></pre>

<p>and found the distribution of F pretty symmetric:</p>

<p><img src='http://snag.gy/QXhqn.jpg' alt='enter image description here' /></p>

<p>and the short summary:</p>

<pre><code>&gt; summary(het$F)
    Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
-0.35990 -0.07199  0.01568  0.02755  0.13460  0.40790
</code></pre>

<p>The F values are quite big (either positive or negative), which made me worry about sample quality. Presumably they are all unrelated. Can anyone tell me whether this distribution of F indicates some problems and what they are? Or, is there a rule of thumb about what F value is considered normal for unrelated, cleaned samples? Thanks!</p>

For relatedness try IBS/IBD estimation:

- plink 1.9 https://www.cog-genomics.org/plink/1.9/ibd
- old website: http://zzz.bwh.harvard.edu/plink/ibdibs.shtml

PI_HAT: 

 - Identical twins, and duplicates, are 100%identical by descent (Pihat 1.0)  
 - First-degree relatives are 50% IBD (Pihat 0.5)  
 - Second-degree relatives are 25% IBD (Pihat 0.25)  
 - Third-degree relatives are 12.5% equal IBD (Pihat 0.125).


