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gaynorr / AlphaSimR

R package for breeding program simulations
https://gaynorr.github.io/AlphaSimR/
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Can recHist tell the grandparental haplotype? #87

Closed jamonterotena closed 1 year ago

jamonterotena commented 1 year ago

I'm running the script for simulating recombinations. recHist is the list that saves the crossover locations in the following way:

CHILD PATERNAL MEIOSIS 2 1 # Haplotype turned 2 in SNP1 (no crossovers) MATERNAL MEIOSIS 2 1 # Haplotype turned 2 in SNP1 (no crossover) 1 130 # Haplotype turned 1 in SNP1 (crossover 2-1) 2 450 # Haplotype turned 2 in SNP450 (crossover 1-2)

I understand that 1/2 accounts for the grandparental origin (the parent paternal or maternal haplotype during meiosis). I would like to know if the numbers have been chosen randomly or if they refer to a certain origin (for example, 1 is the parent's paternal haplotype and 2 is the parent's maternal haplotype). I have seen contradicting results so I cannot understand the logic.

Thanks for your answers

gregorgorjanc commented 1 year ago

@jamonterotena see explanation in https://github.com/gaynorr/AlphaSimR/issues/34

You might also want to look at the IBD functionality.