Existence of a transmitted (or non-transmitted) singleton in at least one of the given families (transmittedSingleton, nonTransmittedSingleton)

Category Variant Annotations

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Overview

Existence of a transmitted or non-transmitted singleton in at least one of the given families

This annotation uses the genotype information from individuals in family trios to identify transmitted and non-transmitted singletons and the sample(s) in which they occur. Transmitted singletons occur at sites in a cohort where the allele count is two and these two alleles occur in one parent and the child of a trio. A non-transmitted singleton are sites with an allele count of one and this one allele occurs in a parent, but not the child of a trio. In both cases the other parent must have a high quality hom ref call.

Caveats

• The calculation assumes that the organism is diploid.
• This annotation requires a valid pedigree file.
• This annotation is only valid for trios, not quads or other more complicated family structures.
• Only reports possible singletons for families where each of the three samples has high GQ (>20) and high depth (>20)
• Only reports possible singletons at sites with a Call Rate greater than 90% (meaning less than 10% of the samples at the given site were no-calls)

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GATK version 4.6.0.0 built at Sat, 29 Jun 2024 20:47:29 -0400.