Best practice for Multiparent population (half-sibs)?

[jjdevega]

Hi,
THanks for developing this package.

We have a multiparent heterozygous autotetraploid population with four families, one shared pollen donor and four mums, so offspring is half siblings. Our input went into polyRAD is a filtered VCF with ok data, and we generated genotype probabilities individually for each family (four files). Offspring per family is uneven and we would benefit by "joining" the families somehow in any downstream step. Is there a better way to work with these families than one at the time?

Thanks

[mmollina]

@jjdevega: Although MAPpoly V-0.3.2 does not support multi-parental populations, I have some research codes that can help you. I am working on a model that estimates a consensus map given the parents' order and phase configuration. Thus, if you managed to build the maps within each full-sib, you can join them downstream. I tested this algorithm in potato, alfalfa, and sweetpotato, and it worked well. I still need to make some final tweaks, but by mid-December, I will upload it into a new branch in this repository.
You will probably need to deal with some bugs in this early stage of development, but I will help you.
Also, have you tried using updog for genotype calling? I suppose that for VCFs with know pedigree, it works better than polyRAD.