Documentation

MVLikelihoodRatio

Likelihood of being a Mendelian Violation

Category Variant Annotations

VCF Field INFO (variant-level)

Type RodRequiringAnnotation


Overview

Given a variant context, this tool uses the genotype likelihoods to assess the likelihood of the site being a mendelian violation versus the likelihood of the site transmitting according to mendelian rules.

Caveats

This tool assumes that the organism is diploid.

Note that this annotation requires a valid ped file.

When multiple trios are present, the annotation is simply the maximum of the likelihood ratios, rather than the strict 1-Prod(1-p_i) calculation, as this can scale poorly for uncertain sites and many trios.

This annotation can only be used from the Variant Annotator. If you attempt to use it from the UnifiedGenotyper, the run will fail with an error message to that effect. If you attempt to use it from the HaplotypeCaller, the run will complete successfully but the annotation will not be added to any variants.


See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.2-2-gec30cee built at 2014/07/17 17:54:48. GTD: NA