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 and ordering proceedures 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, 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 (http://highmap.biomarker.com.cn/) 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.
Hi Rim Gubaev , I have a bit of experience linkage mapping from a RAD dataset and after having some similar problems with some R packages I gave Lepmap a try (https://sourceforge.net/p/lep-map3/wiki/LM3%20Home/). I used LepMAP2 and although a new version LepMAP3 is out perhaps the scripts I used (scripts: https://github.com/RishiDeKayne/WhitefishLinkageMap and methods from the associated paper: https://www.g3journal.org/content/8/12/3745.abstract) would help? LepMAP is designed for really big datasets so yours should be no problem and you can even combine families if needed - additionally I think you might be able to impute some of the missing data which would also help get more out of your genotype dataset in your case! Good luck, Rishi
Hi Rim,
I only used Joinmap. It is not the fasted and cheapest software, but gave good results. But for QTL mapping you still need MapQTL.