I have a large SNP dataset (~6K) derived from GBS sequencing of F2 intercross population and I face a problem of genetic map construction which is needed for subsequent QTl-maping. I tried famous R/qtl but first, it works quite slow, second, it does not produce a proper result in terms of marker order (after all filters I obtain huge chromosomes of >400 cM). Since originally it was constructed smaller marker sets like SSR-derived ones and for very high-quality markers while GBS data is noisy and has a lot of missing values a sequence mistakes etc.
I also tried to use ASMap and onemap R packages, but first one does not support F2 populations (only Backcross (BC), DoubledHaploid (DH) and Recombinant Inbred (RIL) are available) and the second one works similar to R/qtl.
I also wanted to use HighMap but it seems like their webpage is dead now.
If you faced such problems while working with large noisy GBS-dataset to construct a genetic linkage map please share your experience.