Rationale behind convert2riself genotype conversion

[Nathaniel Burner]

Hi Karl,

I am working with a RIL population and was considering using the convert2riself function on my cross. I think I can understand why the AB calls would be omitted when BB > AB, but what is the rationale behind converting AB calls to BB when BB < AB? Thank you for the clarification.

Nathaniel

[Karl Broman]

Just trying to guess at which are the correct genotype labels.

Most commonly, the data initially get treated as a backcross, with AA/AB genotypes, so in converting to RIL, we flip AB -> BB.

karl