Linkage mapping with half-sib population without parental genotypes

[Esteban]

Dear Pasi,

I have a population of half-sib trees, but the parental genotypes are not available, and I would like to perform a linkage mapping analysis using this software. Is it possible to do this with such data?

If so, how should I structure the pedigree file? I have tried, but I get the following error:
Error 520 — Error: No parent(s) in a family CHR:0.

Also, can I use a genotype panel coded as 0, 1, 2, or should it be formatted differently?

Thank you very much for your help.

Best,
Esteban

[Pasi Rastas]

Dear Esteban,

Thank you for your message!

Yes, you can probably construct linkage map from this data. However, you have to provide a pedigree with full-sib families (both parents). You just don't provide any data for the parents you do not have. I think the error you get indicated that the pedigree is missing the parents.

The 0, 1, 2 genotypes must be formatted to Lep-MAP3 likelihoods, assuming 0 and 2 are homozygotes:

0 => 1 0 0 0 0 0 0 0 0 0
1 => 0 1 0 0 0 0 0 0 0 0
2 => 0 0 0 0 1 0 0 0 0 0

These three likelihoods corresponds to AA, AC and CC genotypes, respectively. There are some conversion scripts provided with Lep-MAP3, but I think none of them work with numeric genotypes directly.

Cheers,
Pasi