.org/package=fitPoly" class="external-link"><code>fitPoly</code></a>, or
<a href="https://github.com/guilherme-pereira/vcf2sm" class="external-link"><code>SuperMASSA</code></a>.
Note that GATK uses a uniform prior, so would be inappropriate for
use in <code>ldfast()</code>.</p>
<p>Calculating standard errors and performing hierarchical shrinkage of the
reliability ratios are both rather slow operations compared to just
raw method-of-moments based estimation for LD. If you don't need
standard errors, you can