PossibleDeNovo

Existence of a de novo mutation in at least one of the given families (hiConfDeNovo, loConfDeNovo)

Category Variant Annotations

Overview

Existence of a de novo mutation in at least one of the given families

This annotation uses the genotype information from individuals in family trios to identify possible de novo mutations and the sample(s) in which they occur. This works best if the genotypes have been processed according to the Genotype Refinement workflow.

Caveats

The calculation assumes that the organism is diploid.
This annotation requires a valid pedigree file.
Only reports possible de novos for children whose genotypes have not been tagged as 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.

PossibleDeNovo specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s)	Default value	Summary
Optional Tool Arguments
--denovo-depth-threshold	0	Minimum depth (DP) for all trio members to be considered for de novo calculation.
--denovo-parent-gq-threshold	20	Minimum genotype quality for parents to be considered for de novo calculation (separate from GQ thershold for full trio).

Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.

--denovo-depth-threshold

Minimum depth (DP) for all trio members to be considered for de novo calculation.

int 0 [ [ -∞ ∞ ] ]

--denovo-parent-gq-threshold

Minimum genotype quality for parents to be considered for de novo calculation (separate from GQ thershold for full trio).

int 20 [ [ -∞ ∞ ] ]

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GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.