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alachins / raisd

RAiSD: software to detect positive selection based on multiple signatures of a selective sweep and SNP vectors
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Question on missing data management #54

Open jbruxaux opened 1 month ago

jbruxaux commented 1 month ago

Hi!

I have a quick question on the different ways to handle missing data with RAiSD. As far as I understand, the default behavior (0) is to discard entirely any SNP with any amount of missing data. Option 1 imputes any missing data. How is it done? Based on the allele frequency at this position? Only that or other parameters (nearby SNPs...)? And I'm not sure to really understand options 2 and 3, or rather, what's the difference between them?

Thanks for your help!

Jade