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 index 290e5e896f2..4cba3860b47 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/InbreedingCoeff.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/InbreedingCoeff.java @@ -30,8 +30,12 @@ * higher the chance that some samples are related. If samples are known to be related, a pedigree file can be provided so * that the calculation is only performed on founders and offspring are excluded.

* - *

Statistical notes

- *

The calculation is a continuous generalization of the Hardy-Weinberg test for disequilibrium that works well with limited coverage per sample. The output is a Phred-scaled p-value derived from running the HW test for disequilibrium with PL values. See the method document on statistical tests for a more detailed explanation of this statistical test.

+ *

Details

+ *

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 cosanguinuity is the only source of deviation from Hardy-Weinberg equilibrium. + * If this assumption is not true F may be negative and the excess heterozygosity often indicates an artifactual variant. + * 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.

* *

Caveats

*