How to construct a genetic map by association population ?

Question

[panly89]

Now, I have a RAD-seq data of soybean cultivates, I want to construct a genetic map to find some chromosome variation ,like inversion or translation , which software can do this ? thank you ~~

Answer 1

[berge2015]

If the lines are nicely related to each other (sibs, RILs, etc), you could try making pedigree-based map. If not, you'll have to align your sequences to the Glycine max genome to get the map for each line and other details. Then you can either merge the maps, or just use the sequence/marker order reported on the reference genome.

I doubt you will find a single software to do all of it. Here are some programs that will get you started:

• Bowtie/bwa + Samtools
• Tassel
• Stacks
• inveRsion

[panly89]

Thank you very much,now I have the physical map from the reference genome , I want use the population that unrelated to each other to calculate the recombination rate to search the chromosome variation, how can I do this ? I haven't do this work before.Thank you ~