Entering edit mode
2.2 years ago
Claire
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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
it depends of the context, for example see: https://en.wikipedia.org/wiki/Rare_functional_variant
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?
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.
Got you, thanks Pierre.