What tools to use for genetic map construction or marker ordering using large SNP datasets?

Question

[rimgubaev]

Dear all,

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.

[Asaf]

I have had a good experience with R/qtl with GBS but only a few hundreds of markers. Maybe you should QC the markers first (and make sure they are sorted).

[julian.taylor]

Actually, ASMap does handle F2 populations. After reading your data in using read.cross() from the qtl package, you just need to use convert2bcsft() for ASMap to understand what level of selfing the population is. See mstmap.cross documentation in the package.