<p>Hi,</p>

<p>Is it possible in plink to specify a non-human chromosome in the map file? I am curious if it can be run on a bacterial data set that only has 2 chromosomes and is haploid?</p>

<p>On the site it says:</p>

<pre><code>By default, each line of the MAP file describes a single marker and must contain exactly 4 columns:

 chromosome (1-22, X, Y or 0 if unplaced)
 rs# or snp identifier
 Genetic distance (morgans)
 Base-pair position (bp units)
</code></pre>

<p>However, what if I just label everything chromosome 1 or 2?</p>

<p>Thanks!</p>

<p>If you read about the types of analysis that PLINK can do at the website, it's pretty clear that it's designed for humans. Or at least, diploid organisms which reproduce sexually, have chromosomes that undergo recombination and have sub-populations defined by SNPs. I'd also question whether bacteria even have SNPs in any meaningful sense.</p>
