https://www.popgen.dk/angsd/index.php?action=history&feed=atom&title=SNP_CallingSNP Calling - Revision history2026-05-12T00:16:10ZRevision history for this page on the wikiMediaWiki 1.40.1https://www.popgen.dk/angsd/index.php?title=SNP_Calling&diff=169&oldid=prevThorfinn at 10:34, 19 June 20122012-06-19T10:34:01Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:34, 19 June 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1">Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>angsd can estimate and LRT for the site being variable. This works in tandem with -doMAF and -doMajorMinor.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>angsd can estimate and LRT for the site being variable. This works in tandem with -doMAF and -doMajorMinor.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The MAF <del style="font-weight: bold; text-decoration: none;">Toptimizes </del>a likelihood and this likelihood can also be used for SNP discovery. This is done by estimating the likelihood under the alternative model (optimized likelihood), and under a null model where only one allele is present. This gives us an like lihood ratio test statistic (LRT) that is chrsquare distributed with one degree of freedom and can be converted to a p-value. An LRT of 10^-6 correspond to a pvalue of 10^-6.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The MAF <ins style="font-weight: bold; text-decoration: none;">optimizes </ins>a likelihood and this likelihood can also be used for SNP discovery. This is done by estimating the likelihood under the alternative model (optimized likelihood), and under a null model where only one allele is present. This gives us an like lihood ratio test statistic (LRT) that is chrsquare distributed with one degree of freedom and can be converted to a p-value. An LRT of 10^-6 correspond to a pvalue of 10^-6.</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">For every MAF estimator selected the program will print out the corresponding LRT value for that estimator</ins></div></td></tr>
</table>Thorfinnhttps://www.popgen.dk/angsd/index.php?title=SNP_Calling&diff=168&oldid=prevThorfinn at 10:33, 19 June 20122012-06-19T10:33:18Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:33, 19 June 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1">Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>angsd can estimate and LRT for the site being variable. This works in tandem with -doMAF and -doMajorMinor.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>angsd can estimate and LRT for the site being variable. This works in tandem with -doMAF and -doMajorMinor.</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">The MAF Toptimizes a likelihood and this likelihood can also be used for SNP discovery. This is done by estimating the likelihood under the alternative model (optimized likelihood), and under a null model where only one allele is present. This gives us an like lihood ratio test statistic (LRT) that is chrsquare distributed with one degree of freedom and can be converted to a p-value. An LRT of 10^-6 correspond to a pvalue of 10^-6.</ins></div></td></tr>
</table>Thorfinnhttps://www.popgen.dk/angsd/index.php?title=SNP_Calling&diff=165&oldid=prevThorfinn: Created page with "angsd can estimate and LRT for the site being variable. This works in tandem with -doMAF and -doMajorMinor."2012-06-19T10:15:12Z<p>Created page with "angsd can estimate and LRT for the site being variable. This works in tandem with -doMAF and -doMajorMinor."</p>
<p><b>New page</b></p><div>angsd can estimate and LRT for the site being variable. This works in tandem with -doMAF and -doMajorMinor.</div>Thorfinn