clarify

davidbenjamin · davidbenjamin · commit dfdca101895e · 2019-03-06T14:50:34.000-05:00
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/InbreedingCoeff.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/InbreedingCoeff.java
@@ -31,7 +31,8 @@
  * that the calculation is only performed on founders and offspring are excluded.</p>
  *
  * <h3>Details</h3>
- * <p>The output is the inbreeding coefficient 'F' (fixation) score, which is equal to the probability that an individual's two alleles are identical by descent.
+ * <p>The output is the inbreeding coefficient 'F' (fixation) statistic, which for large sample sizes converges to the probability
+ * that an individual's two alleles are identical by descent, provided that inbreeding is the only source of deviation from Hardy-Weinberg equilibrium.
  * It is calculated as F = 1 - (# of het genotypes)/(# of het genotypes expected under Hardy-Weinberg equilibrium).  The number of het genotypes expeced under Hardy-Weinberg equilibrium
  * is 2*(# of samples)*(ref allele frequency)*(alt allele frequency), where allele frequencies are calculated from the samples' genotypes.</p>
  *

Original file line number	Diff line number	Diff line change
`@@ -31,7 +31,8 @@`
`31`	`31`	`* that the calculation is only performed on founders and offspring are excluded.</p>`
`32`	`32`	`*`
`33`	`33`	`* <h3>Details</h3>`
`34`		`- * <p>The output is the inbreeding coefficient 'F' (fixation) score, which is equal to the probability that an individual's two alleles are identical by descent.`
	`34`	`+ * <p>The output is the inbreeding coefficient 'F' (fixation) statistic, which for large sample sizes converges to the probability`
	`35`	`+ * that an individual's two alleles are identical by descent, provided that inbreeding is the only source of deviation from Hardy-Weinberg equilibrium.`
`35`	`36`	`* It is calculated as F = 1 - (# of het genotypes)/(# of het genotypes expected under Hardy-Weinberg equilibrium). The number of het genotypes expeced under Hardy-Weinberg equilibrium`
`36`	`37`	`* is 2(# of samples)(ref allele frequency)*(alt allele frequency), where allele frequencies are calculated from the samples' genotypes.</p>`
`37`	`38`	`*`