GBS-Tassel-JoinMap

[Nima Samadi]

Hi everyone, 

Does anyone have any experience in working with JoinMap? 

I tried to learn it by using its tutorial PDF. Now I know how it works, but I need help using it for my own data. 

So, I am working on a GBS-GWAS (tassel) project, where my samples are diploid potatoes. 

I already ran the GBS with Linux (Command line), and as the output, I had a vcf file that contained my SNP data. In the next step, I had my SNP data in the tassel for a genome-wide association study. 

Now, I want to use my SNP data in the joinmap, but I need to learn how to have the correct input data format for joinmap. 

By the way, I need to set my population parameter's type in the joinmap as CP since it is cross-pollinated. so, I am guessing that my file format should show my SNPs as lm & ll? 

Please let me know if you have any experience with that. 

Thanks 

Nima