PossibleDeNovo

Tags variants with called genotypes that support the existence of a de novo mutation in at least one of the given families

Category Variant Annotations

VCF Field INFO (variant-level)

Type ExperimentalAnnotation, RodRequiringAnnotation


Overview

Given a variant context, this tool uses the called genotypes (ideally after having been refined using PhaseByTransmission and CalculateGenotypePosteriors) to identify possible de novo mutations and the sample in which they occur.

Caveats

This tool assumes that the organism is diploid.

Note that this annotation requires a valid ped file.

Only reports possible de novos for children where genotype is not filtered (which is most appropriate if parent likelihoods have already been factored in using PhaseByTransmission).

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 2014/09/12 22:29:29. GTD: NA