Filtering imputed vcf files based on probability scores

Question

[Floris Brenk]

Dear all,

I'm looking for some parameters to filter my genotypes after imputation with the imputation server (https://imputationserver.sph.umich.edu/) which I can really recommend by the way... There are already topics like this about vcf filtering: Filtering Imputation output: how to filter on a VCF INFO field and this Filtering Vcf File, but non specific for the DS and GP value...

DS,Number=1,Type=Float,Description="Estimated Alternate Allele Dosage : [P(0/1)+2*P(1/1)] ">

GP,Number=3,Type=Float,Description="Estimated Posterior Probabilities for Genotypes 0/0, 0/1 and 1/1 ">

I already filter at a later step for variants with an R2 >0.3. What would be appropriate filter for the DS and the GP? Since I assume genotypes with low values are not really trustworthy...

[TriS]

I'm not sure you need to filter for DS and GP, after filtering for R^2>0.3 you can filter based on phred values and that should be enough.

[Shicheng Guo]

How do select the best threshold for this R2? 0.3, 0.5, 0.9?