What to do with missing data when constructing a SFS

[jkonva...@gmail.com]

Hello everyone,

I'm trying to construct a SFS from my SNP data but have quite a bit of missing data. For some SNPs there is no data for my outgroup, meaning I'm not sure what the ancestral allele is. Does this mean I should just throw out those SNPs?

The other problem is that I have many individuals that have missing data for specific SNPs. Do I remove those individuals from the SNP-specific analyses?

Thank you in advance for your help.

Sincerely,
Johnny

[Laurent Excoffier]

Hi,

you need to have no missing data among your individuals to compute the sfs.

Removing some individuals with lots of missing data can be a solution.

Imputation is another solution, even though I do not like this idea very much... it might lead to biased demographic estimation if imputation is just based on major alleles

best

laurent