My group has constructed a successful PHG from a grouping of 26 NAM founders and 11 Teosinte pseudogenomes. However, we're grappling with a lower presence of B73 5.0 (the reference used with the PHG) in our imputed haplotype percentages than what we've been expecting.
Below are some imputation specific questions for the folks at the Buckler lab:
- During our consensus haplotype step, none of the ~18,000 gamete_groups of 111046 shared haplotypes included the foundational reference. Is the reference used to construct the PHG not included in consensus haplotype extraction?
- Having conducted imputation on a single lines and groups. I've notice the paths returned for a specific line differs on how many other lines are in the imputation keyfile. If submitted together, are the paths for lines not calculated independently?
- For the data we are currently imputing, I notice we have the choice between the Viterbi algorithm and forward-backward algorithm, would you have a recommendation between the two?
Thank you for your time.
Peter - thanks for responding and clarifying for TIm. Tim - Peter is the guru of this code so believe everything he says!