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Notes: <br> Sites with more than two alleles (not including REF_ALLELE) will be discarded  
 
Notes: <br> Sites with more than two alleles (not including REF_ALLELE) will be discarded  
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To-Do: <br>  ** Include genotypes only for individuals that have sequence data
    
== (10) Run thunder (hidden Markov model) ==
 
== (10) Run thunder (hidden Markov model) ==
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