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nb/vcf.html

@@ -3940,7 +3940,7 @@ <h1 id="comparison-of-vcf-files">Comparison of VCF files<a class="anchor-link" h
 <p>In order to count the genotypes for the matching positions we can use once again <code>bcftools filter</code>  command. Only that this time we will filter based on the genotype columns for the two samples (GT[0] and GT[1]). GT[0] repesents the genotype for the first sample in the merge command and GT[1] is the genotype for the second sample in the merge command.</p>
 <ul>
 <li>AR - heterozygous</li>
-<li>AA - heterozygous alternate</li>
+<li>AA - homozygous alternate</li>
 </ul>
 <p>For example, the filter <code>GT[0]="AR" &amp;&amp; GT[1]="AR"</code> will keep only position in which both samples have a heterozygous genotype.
 A quick way to count how many positions are in the VCF file is by suing the simple bash command <code>grep</code>. This will count all the lines in the VCF files that do not start with a <code>#</code>, thus all the data lines.</p>

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