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De Novo Scoring

The Small Pedigree Workflow app performs de novo calling for the proband sample if the pedigree includes one proband and both parents. This flags variants that are likely to be de novo variants (present in neither parent). The de novo quality score (DQ FORMAT field) is reported to the sample column in the proband (g)vcf file, and in the proband sample column in the multi-sample vcf file.

SNVs and indels undergo DQ scoring if all the following criteria are met for all three trio samples:

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Genotypes (GT FORMAT field) is present

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Genotype likelihoods (PL FORMAT field) are present

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Sample filter (FT FORMAT field) is present and set to PASS in all relevant samples

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Variant FILTER field is PASS or missing, indicating a passing variant call

Sites that do not undergo DQ scoring do not have a DQ FORMAT field. SNVs and Indels are considered de novo if they pass filters and have a DQ ≥ 7. SVs are considered de novo if they pass filters and have a DQ ≥ 20.

For Research Use Only. Not for use in diagnostic procedures.