What are the steps for QTL analysis?

Question

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Hello, a question from a newbie:

how to do QTL analysis in mice? GEMMA gave me the following (.assoc.txt) output:

    chr  rs           ps       n_miss  allele1  allele0  af     logl_H1        l_mle         p_lrt  
    1    UNC6         3010274  45      T        C        0.753  -1.871575e+03  9.092954e+00  4.497885e-01...

I suppose I have to do the following:

1) to draw a Manhattan plot with 5×10^(−8) as a genomewide cutoff;
2) to make an 95% CI for each (?) significant SNP;
3) to search for and list the linked genomic regions.

A fantastic tool FUMA exists but only for GWAS in humans I guess...

Any suggestion on a tutorial or a tool for this task is appreciated.