I am analyzing genome-wide genotyping data from 200 F2 individuals from 4 different mice families, derived from a cross between the C57BL/6 (B6) strain (an inbred strain characterized by homozygosis at every genetic locus) and a particular outbred strain (derived from the cross of 7 different inbred strains), which has some loci in heterozygosis.
Since one of the parents is outbred, the alleles of the F2 individuals at each genotyped SNP do not show the typical 1:2:1 ratios. However, this mice population neither displays the same degree of genetic heterogeneity of a human one.
Our plan is to carry out a genome-wide eQTL analysis to find which loci are in linkage with the expression levels of particular genes. However, the tool we used to this aim in the past (R/qtl) is not able to account for such alleles ratios. Does anyone know any bioinformatics tools which can be used for a linkage analysis in such a population, and whose use can be easily automatized via R, Pyton or bash scripts?