Skip to content

corrected javadoc for InbreedingCoeff #5768

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 4 commits into from
Mar 7, 2019
Merged

corrected javadoc for InbreedingCoeff #5768

Changes from 3 commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
956eec6
corrected javadoc for InbreedingCoeff
davidbenjamin Mar 6, 2019
dfdca10
clarify
davidbenjamin Mar 6, 2019
2e123d4
more clarify
davidbenjamin Mar 6, 2019
e334ca3
cosanguinuity
davidbenjamin Mar 7, 2019
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 6 additions & 2 deletions src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/InbreedingCoeff.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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.</p>
*
* <h3>Statistical notes</h3>
* <p>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 <a href="http://www.broadinstitute.org/gatk/guide/article?id=4732">method document on statistical tests</a> for a more detailed explanation of this statistical test.</p>
* <h3>Details</h3>
* <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.
* 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.</p>
*
* <h3>Caveats</h3>
* <ul>
Expand Down