Extended trios -- multiple generations

[campanam]

Allow extension of trios to at least grandparents to observe heritability

[campanam]

Hackey Solution

1. Run grandchildren/parents first
2. Run grandparents/parents second with optional parameter pointing to grandchildren/parents combined VCF
3. Profit (compare DNM candidates to grandchildren/parents VCF)

[campanam]

Alternatively, specify configuration thusly:
params.f1_sire # Equivalent to f0, sire of f1
params.f1_dam
params.f1_offspring
params.f2_offspring
params.f2_sire # Sire of f2
params.f2_dam

Could even do array inputs if multiple branches of family tree

e.g

params.f1_sire = Ind1,Ind9
params.f1_dam = Ind2
params.f1_offspring = [Ind3,Ind4,Ind5],[Ind6,Ind7,Ind8]
params.f2_sire = Ind8
params.f2_dam = Ind11,Ind12
params.f2_offspring=[Ind13,Ind14,Ind15],[Ind16,Ind17,Ind18]

Everything would match up by index. So Ind3,Ind4,Ind5 would have parents Ind1 and Ind2. Ind6-8, Ind2 and Ind9. Something along these lines.

[campanam]

Alternatively, read PLINK file to auto-detect trios

[campanam]

Best option is PLINK --ped format then have trios automatically subdivided after WhatsHap phasing. Good development for next major release (1.3.0 or 2.0.0 depending on how much restructuring needed).