Running dadi using variant-only vcf as input?

[Isaac Linn]

Sorry if this is a simple question, but I haven't found a clear answer so far.

I'm going through the process of running dadi on a population dataset for which I have a SNP-only VCF. I can go through the process of variant calling again, but at present, I don't have access to a VCF with variant and invariant sites. I'm wondering whether I can use dadi with this input only, whether I need to pad the dataset with monomorphic sites, or whether it's not an issue. I've tried running dadi so far and population size estimates look way low when I use L=length of callable input sequence, but when I use L= number of sites in VCF (again, mostly polymorphic) the population size estimates are a reasonable order of magnitude (compared with nucleotide diversity). 

I think I understand that the monomorphic sites would not make it into the allele frequency spectrum, but I'm concerned that it would impact the underlying model or estimation of theta. 

Thanks,

Isaac

[Ryan Gutenkunst]

Hello Isaac,

Yes, dadi will work fine with a variant-only vcf; it will not impact the model or estimation of theta compared to an all-sites VCF.

Estimating L is sometimes tricky, depending on how the sequencing was done. It may be that certain regions were uncallable or masked (for example, repetitive regions), so L is rarely the full genome size. Setting L equal to the number of variant sites is a mistake.

Best,

Ryan

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