Missing genotypic information in 4-way cross

[Lise H]

Hi,

I have three F2 populations from interspecific crosses of the outcrossing species Arabidopsis lyrata. I have the genotypes for the parental individuals and the F2 offspring, but I do not have genotypic information from the F1s. I am planning to create one map per F2 population. I understand I can use the 4-way cross implemented in rQTL, but is there a way to work around the issue of missing the F1 genotypic information? I am not sure how to transform the genotypes in the vcf file to the rQTL input file.

Cheers,

Lise

[Karl Broman]

For the “4way” cross type in R/qtl, you need to infer phase in each individual, which means determining which of the 4 founders gave each allele in each individual. You don’t need to know the F1 genotypes, though it would be helpful, and you’ll pretty much be inferring it as part of the process. 

karl