How to interpret singleton and doubleton?
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3 months ago
Claire • 0

Hi everyone This is a naiive question for a newbie. I understand what is the meaning of a singleton and a doubleton SNP and can count them using vcftools. But I don't understand what knowledge we will get by knowing how much we have of them in a VCF of multiple individuals. Like how can I interpret some numbers of singleton and doubleton I have.

Thank you

Singletons Doubletons • 404 views
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it depends of the context, for example see: https://en.wikipedia.org/wiki/Rare_functional_variant

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I understand rare variants. Use annovar to filter the vcf for gnomad <0.1. But does a singleton counts as rare? It could be singleton in this individual but not in population?

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it depends of the number of samples in your vcf it can also be used as a control for your vcf. If your sample has too many singletons, then you should have a look at its' origin (population...) or / and its' quality.

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Got you, thanks Pierre.

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