http://genome.sph.umich.edu/w/index.php?title=Minimac3_Info_(Older_Version)&feed=atom&action=historyMinimac3 Info (Older Version) - Revision history2024-03-28T23:10:03ZRevision history for this page on the wikiMediaWiki 1.35.9http://genome.sph.umich.edu/w/index.php?title=Minimac3_Info_(Older_Version)&diff=13873&oldid=prevSanty.8128 at 21:51, 19 October 20152015-10-19T21:51:53Z<p></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" 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 21:51, 19 October 2015</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>'''If you downloaded Minimac3 version earlier than 0.1.13 (can check the LOG file; source code downloaded before Oct 15, 2015 or imputed data downloaded from Imputation Server) please see this page for Info File descriptors. If using version 0.1.13 or above, please see [[Minimac3 Info File | new version of Minimac3 Info page]]''' !!!</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>'''If you downloaded Minimac3 version earlier than 0.1.13 (can check the LOG file; source code downloaded before Oct 15, 2015 or imputed data downloaded from Imputation Server) please see this page for Info File descriptors. If using version 0.1.13 or above, please see [[Minimac3 Info File | new version of Minimac3 Info page]]''' !!!</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;"></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;"></td></tr>
<tr><td class='diff-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>['''P.S.''' There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file just makes it easier for users to determine the minor allele in their imputed data. In the earlier versions, we only reported the minor allele frequency (MAF) of the imputed data in the info file, while the minor and major alleles reported in the info file were major/minor alleles with respect to the reference panel allele frequency and NOT imputed data allele frequency. As a result, the users only had the MAF of their imputed data in their info files but NO way of knowing which one was the minor allele in the imputed data (although most of the times we have the same major/minor alleles between the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5). In the new version, we report the REF and ALT alleles and the ALT allele frequency along with MAF; thus comparing the MAF with the alternate allele frequency, one can easily determine the minor allele in the their imputed data. '''For users with this earlier version of info file, there is NO need to re-run the imputation.''' The imputed data is same. And if you need to determine the minor allele in your imputed data, you just need to calculate the MAF on your side from the imputed data. Please contact [mailto:sayantan@umich.edu Sayantan Das] for any queries <del class="diffchange diffchange-inline">we </del>have. We, the authors of Minimac3, apologize for any inconvenience caused due to these updates.</div></td><td class='diff-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>['''P.S.''' There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file just makes it easier for users to determine the minor allele in their imputed data. In the earlier versions, we only reported the minor allele frequency (MAF) of the imputed data in the info file, while the minor and major alleles reported in the info file were major/minor alleles with respect to the reference panel allele frequency and NOT imputed data allele frequency. As a result, the users only had the MAF of their imputed data in their info files but NO way of knowing which one was the minor allele in the imputed data (although most of the times we have the same major/minor alleles between the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5). In the new version, we report the REF and ALT alleles and the ALT allele frequency along with MAF; thus comparing the MAF with the alternate allele frequency, one can easily determine the minor allele in the their imputed data. '''For users with this earlier version of info file, there is NO need to re-run the imputation.''' The imputed data is same<ins class="diffchange diffchange-inline">. Only the info files have slightly different formats</ins>. And if you need to determine the minor allele in your imputed data, you just need to calculate the MAF on your side from the imputed data. Please contact [mailto:sayantan@umich.edu Sayantan Das] for any queries <ins class="diffchange diffchange-inline">you </ins>have. We, the authors of Minimac3, apologize for any inconvenience caused due to these updates.</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;"></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;"></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>= Introduction =</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>= Introduction =</div></td></tr>
</table>Santy.8128http://genome.sph.umich.edu/w/index.php?title=Minimac3_Info_(Older_Version)&diff=13872&oldid=prevSanty.8128 at 21:50, 19 October 20152015-10-19T21:50:18Z<p></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" 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 21:50, 19 October 2015</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>'''If you downloaded Minimac3 version earlier than 0.1.13 (can check the LOG file; source code downloaded before Oct 15, 2015 or imputed data downloaded from Imputation Server) please see this page for Info File descriptors. If using version 0.1.13 or above, please see [[Minimac3 Info File | new version of Minimac3 Info page]]''' !!!</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>'''If you downloaded Minimac3 version earlier than 0.1.13 (can check the LOG file; source code downloaded before Oct 15, 2015 or imputed data downloaded from Imputation Server) please see this page for Info File descriptors. If using version 0.1.13 or above, please see [[Minimac3 Info File | new version of Minimac3 Info page]]''' !!!</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;"></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;"></td></tr>
<tr><td class='diff-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>['''P.S.''' There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file makes it easier for users to determine the minor allele in their imputed data. In the earlier versions, we only reported the minor allele frequency (MAF) of the imputed data in the info file, while the minor and major alleles reported in the info file were major/minor alleles with respect to the reference panel allele frequency and NOT imputed data allele frequency. As a result, the users only had the MAF of their imputed data in their info files but NO way of knowing which one was the minor allele in the imputed data (although most of the times we have the same major/minor alleles between the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5). In the new version, we report the REF and ALT alleles and the ALT allele frequency along with MAF; thus comparing the MAF with the alternate allele frequency, one can easily determine the minor allele in the their imputed data. '''For users with this earlier version of info file, there is NO need to re-run the imputation.''' <del class="diffchange diffchange-inline">If </del>you need to determine the minor allele in your imputed data, you just need to calculate the MAF on your side. Please contact [mailto:sayantan@umich.edu Sayantan Das] for any queries we have. We, the authors of Minimac3, apologize for any inconvenience caused due to these updates.</div></td><td class='diff-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>['''P.S.''' There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file <ins class="diffchange diffchange-inline">just </ins>makes it easier for users to determine the minor allele in their imputed data. In the earlier versions, we only reported the minor allele frequency (MAF) of the imputed data in the info file, while the minor and major alleles reported in the info file were major/minor alleles with respect to the reference panel allele frequency and NOT imputed data allele frequency. As a result, the users only had the MAF of their imputed data in their info files but NO way of knowing which one was the minor allele in the imputed data (although most of the times we have the same major/minor alleles between the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5). In the new version, we report the REF and ALT alleles and the ALT allele frequency along with MAF; thus comparing the MAF with the alternate allele frequency, one can easily determine the minor allele in the their imputed data. '''For users with this earlier version of info file, there is NO need to re-run the imputation.''' <ins class="diffchange diffchange-inline">The imputed data is same. And if </ins>you need to determine the minor allele in your imputed data, you just need to calculate the MAF on your side <ins class="diffchange diffchange-inline">from the imputed data</ins>. Please contact [mailto:sayantan@umich.edu Sayantan Das] for any queries we have. We, the authors of Minimac3, apologize for any inconvenience caused due to these updates.</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;"></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;"></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>= Introduction =</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>= Introduction =</div></td></tr>
</table>Santy.8128http://genome.sph.umich.edu/w/index.php?title=Minimac3_Info_(Older_Version)&diff=13871&oldid=prevSanty.8128 at 21:45, 19 October 20152015-10-19T21:45:04Z<p></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" 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 21:45, 19 October 2015</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>'''If you downloaded Minimac3 version earlier than 0.1.13 (can check the LOG file; source code downloaded before Oct 15, 2015 or imputed data downloaded from Imputation Server) please see this page for Info File descriptors. If using version 0.1.13 or above, please see [[Minimac3 Info File | new version of Minimac3 Info page]]''' !!!</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>'''If you downloaded Minimac3 version earlier than 0.1.13 (can check the LOG file; source code downloaded before Oct 15, 2015 or imputed data downloaded from Imputation Server) please see this page for Info File descriptors. If using version 0.1.13 or above, please see [[Minimac3 Info File | new version of Minimac3 Info page]]''' !!!</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;"></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;"></td></tr>
<tr><td class='diff-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>['''P.S.''' There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file makes it easier for users to determine the minor allele in their imputed data. In the earlier versions, we only reported the minor allele frequency (MAF) of the imputed data in the info file, while the minor and major alleles reported in the info file were major/minor alleles with respect to the reference panel allele frequency and NOT imputed data allele frequency. As a result, the users only had the MAF of their imputed data in their info files but NO way of knowing which one was the minor allele in the imputed data (although most of the times we have the same major/minor alleles between the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5). In the new version, we report the REF and ALT alleles and the ALT allele frequency along with MAF; thus comparing the MAF with the alternate allele frequency, one can easily determine the minor allele in the their imputed data. '''For users with this earlier version of info file, there is NO need to re-run the imputation. If you need to determine the minor allele in your imputed data, you just need to calculate the MAF on your side. Please contact [mailto:sayantan@umich.edu Sayantan Das] for any queries we have. We, the authors of Minimac3, apologize for any inconvenience caused due to these <del class="diffchange diffchange-inline">updat'''es</del>.</div></td><td class='diff-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>['''P.S.''' There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file makes it easier for users to determine the minor allele in their imputed data. In the earlier versions, we only reported the minor allele frequency (MAF) of the imputed data in the info file, while the minor and major alleles reported in the info file were major/minor alleles with respect to the reference panel allele frequency and NOT imputed data allele frequency. As a result, the users only had the MAF of their imputed data in their info files but NO way of knowing which one was the minor allele in the imputed data (although most of the times we have the same major/minor alleles between the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5). In the new version, we report the REF and ALT alleles and the ALT allele frequency along with MAF; thus comparing the MAF with the alternate allele frequency, one can easily determine the minor allele in the their imputed data. '''For users with this earlier version of info file, there is NO need to re-run the imputation.<ins class="diffchange diffchange-inline">''' </ins>If you need to determine the minor allele in your imputed data, you just need to calculate the MAF on your side. Please contact [mailto:sayantan@umich.edu Sayantan Das] for any queries we have. We, the authors of Minimac3, apologize for any inconvenience caused due to these <ins class="diffchange diffchange-inline">updates</ins>.</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;"></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;"></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>= Introduction =</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>= Introduction =</div></td></tr>
</table>Santy.8128http://genome.sph.umich.edu/w/index.php?title=Minimac3_Info_(Older_Version)&diff=13870&oldid=prevSanty.8128 at 21:44, 19 October 20152015-10-19T21:44:40Z<p></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" 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 21:44, 19 October 2015</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>'''If you downloaded Minimac3 version earlier than 0.1.13 (can check the LOG file; source code downloaded before Oct 15, 2015 or imputed data downloaded from Imputation Server) please see this page for Info File descriptors. If using version 0.1.13 or above, please see [[Minimac3 Info File | new version of Minimac3 Info page]]''' !!!</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>'''If you downloaded Minimac3 version earlier than 0.1.13 (can check the LOG file; source code downloaded before Oct 15, 2015 or imputed data downloaded from Imputation Server) please see this page for Info File descriptors. If using version 0.1.13 or above, please see [[Minimac3 Info File | new version of Minimac3 Info page]]''' !!!</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;"></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;"></td></tr>
<tr><td class='diff-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>['''P.S.''' There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file makes it easier for users to determine the minor allele in their imputed data. In the earlier versions, we only reported the minor allele frequency (MAF) of the imputed data in the info file, while the minor and major alleles reported in the info file were major/minor alleles with respect to the reference panel allele frequency and NOT imputed data allele frequency. As a result, the users only had the MAF of their imputed data in their info files but NO way of knowing which one was the minor allele in the imputed data (although most of the times we have the same major/minor alleles between the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5). In the new version, we report the REF and ALT alleles and the ALT allele frequency along with MAF; thus comparing the MAF with the alternate allele frequency, one can easily determine the minor allele in the their imputed data. Please contact [mailto:sayantan@umich.edu Sayantan Das] for any queries we have. We, the authors of Minimac3, apologize for any inconvenience caused due to these <del class="diffchange diffchange-inline">updates</del>.</div></td><td class='diff-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>['''P.S.''' There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file makes it easier for users to determine the minor allele in their imputed data. In the earlier versions, we only reported the minor allele frequency (MAF) of the imputed data in the info file, while the minor and major alleles reported in the info file were major/minor alleles with respect to the reference panel allele frequency and NOT imputed data allele frequency. As a result, the users only had the MAF of their imputed data in their info files but NO way of knowing which one was the minor allele in the imputed data (although most of the times we have the same major/minor alleles between the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5). In the new version, we report the REF and ALT alleles and the ALT allele frequency along with MAF; thus comparing the MAF with the alternate allele frequency, one can easily determine the minor allele in the their imputed data<ins class="diffchange diffchange-inline">. '''For users with this earlier version of info file, there is NO need to re-run the imputation. If you need to determine the minor allele in your imputed data, you just need to calculate the MAF on your side</ins>. Please contact [mailto:sayantan@umich.edu Sayantan Das] for any queries we have. We, the authors of Minimac3, apologize for any inconvenience caused due to these <ins class="diffchange diffchange-inline">updat'''es</ins>.</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;"></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;"></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>= Introduction =</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>= Introduction =</div></td></tr>
</table>Santy.8128http://genome.sph.umich.edu/w/index.php?title=Minimac3_Info_(Older_Version)&diff=13869&oldid=prevSanty.8128 at 17:21, 19 October 20152015-10-19T17:21:01Z<p></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" 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 17:21, 19 October 2015</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>'''If you downloaded Minimac3 version earlier than 0.1.13 (can check the LOG file; source code downloaded before Oct 15, 2015 or imputed data downloaded from Imputation Server) please see this page for Info File descriptors. If using version 0.1.13 or above, please see [[Minimac3 Info File | new version of Minimac3 Info page]]''' !!!</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>'''If you downloaded Minimac3 version earlier than 0.1.13 (can check the LOG file; source code downloaded before Oct 15, 2015 or imputed data downloaded from Imputation Server) please see this page for Info File descriptors. If using version 0.1.13 or above, please see [[Minimac3 Info File | new version of Minimac3 Info page]]''' !!!</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;"></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;"></td></tr>
<tr><td class='diff-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>['''P.S.''' There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file makes it easier for users to determine the minor allele in <del class="diffchange diffchange-inline">the </del>imputed data. In the earlier versions, we only reported the minor allele frequency (MAF) of the imputed data in the info file, while the minor and major alleles reported in the info file were major/minor alleles with respect to the reference panel allele frequency and NOT imputed data allele frequency. As a result, the users only had the MAF of their imputed data in their info files but NO way of knowing which one was the minor allele in the imputed data (although most of the times we have the same major/minor alleles between the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5). In the new version, we report the REF and ALT alleles and the ALT allele frequency along with MAF; thus comparing the MAF with the alternate allele frequency, one can easily determine the minor allele in the their imputed data. Please contact [mailto:sayantan@umich.edu Sayantan Das] for any queries we have. We, the authors of Minimac3, apologize for any inconvenience caused due to these updates.</div></td><td class='diff-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>['''P.S.''' There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file makes it easier for users to determine the minor allele in <ins class="diffchange diffchange-inline">their </ins>imputed data. In the earlier versions, we only reported the minor allele frequency (MAF) of the imputed data in the info file, while the minor and major alleles reported in the info file were major/minor alleles with respect to the reference panel allele frequency and NOT imputed data allele frequency. As a result, the users only had the MAF of their imputed data in their info files but NO way of knowing which one was the minor allele in the imputed data (although most of the times we have the same major/minor alleles between the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5). In the new version, we report the REF and ALT alleles and the ALT allele frequency along with MAF; thus comparing the MAF with the alternate allele frequency, one can easily determine the minor allele in the their imputed data. Please contact [mailto:sayantan@umich.edu Sayantan Das] for any queries we have. We, the authors of Minimac3, apologize for any inconvenience caused due to these updates.</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;"></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;"></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>= Introduction =</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>= Introduction =</div></td></tr>
</table>Santy.8128http://genome.sph.umich.edu/w/index.php?title=Minimac3_Info_(Older_Version)&diff=13868&oldid=prevSanty.8128 at 17:20, 19 October 20152015-10-19T17:20:10Z<p></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" 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 17:20, 19 October 2015</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>'''If you downloaded Minimac3 version earlier than 0.1.13 (can check the LOG file; source code downloaded before Oct 15, 2015 or imputed data downloaded from Imputation Server) please see this page for Info File descriptors. If using version 0.1.13 or above, please see [[Minimac3 Info File | new version of Minimac3 Info page]]''' !!!</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>'''If you downloaded Minimac3 version earlier than 0.1.13 (can check the LOG file; source code downloaded before Oct 15, 2015 or imputed data downloaded from Imputation Server) please see this page for Info File descriptors. If using version 0.1.13 or above, please see [[Minimac3 Info File | new version of Minimac3 Info page]]''' !!!</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;"></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;"></td></tr>
<tr><td class='diff-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>['''P.S.''' There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file makes it easier for users to <del class="diffchange diffchange-inline">get </del>the minor allele in the imputed data. In the earlier versions, we only reported the minor allele frequency (MAF) of the imputed data in the info file, while the minor and major alleles reported in the info file were major/minor alleles with respect to the reference panel allele frequency and NOT imputed data allele frequency. As a result, the users only had the MAF of their imputed data in their info files but NO way of knowing which one was the minor allele in the imputed data (although most of the times we have the same major/minor alleles between the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5). In the new version, we report the REF and ALT alleles and the ALT allele frequency along with MAF; thus comparing the MAF with the alternate allele frequency, one can easily determine the minor allele in the their imputed data. Please contact [mailto:sayantan@umich.edu Sayantan Das] for any queries we have. We, the authors of Minimac3, apologize for any inconvenience caused due to these updates.</div></td><td class='diff-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>['''P.S.''' There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file makes it easier for users to <ins class="diffchange diffchange-inline">determine </ins>the minor allele in the imputed data. In the earlier versions, we only reported the minor allele frequency (MAF) of the imputed data in the info file, while the minor and major alleles reported in the info file were major/minor alleles with respect to the reference panel allele frequency and NOT imputed data allele frequency. As a result, the users only had the MAF of their imputed data in their info files but NO way of knowing which one was the minor allele in the imputed data (although most of the times we have the same major/minor alleles between the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5). In the new version, we report the REF and ALT alleles and the ALT allele frequency along with MAF; thus comparing the MAF with the alternate allele frequency, one can easily determine the minor allele in the their imputed data. Please contact [mailto:sayantan@umich.edu Sayantan Das] for any queries we have. We, the authors of Minimac3, apologize for any inconvenience caused due to these updates.</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;"></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;"></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>= Introduction =</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>= Introduction =</div></td></tr>
</table>Santy.8128http://genome.sph.umich.edu/w/index.php?title=Minimac3_Info_(Older_Version)&diff=13867&oldid=prevSanty.8128 at 17:19, 19 October 20152015-10-19T17:19:40Z<p></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" 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 17:19, 19 October 2015</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>'''If you downloaded Minimac3 version earlier than 0.1.13 (can check the LOG file; source code downloaded before Oct 15, 2015 or imputed data downloaded from Imputation Server) please see this page for Info File descriptors. If using version 0.1.13 or above, please see [[Minimac3 Info File | new version of Minimac3 Info page]]''' !!!</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>'''If you downloaded Minimac3 version earlier than 0.1.13 (can check the LOG file; source code downloaded before Oct 15, 2015 or imputed data downloaded from Imputation Server) please see this page for Info File descriptors. If using version 0.1.13 or above, please see [[Minimac3 Info File | new version of Minimac3 Info page]]''' !!!</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;"></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;"></td></tr>
<tr><td class='diff-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>['''P.S.''' There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file makes it easier for users to get the minor allele in the imputed data. In the earlier versions, we only reported the minor allele frequency of the imputed data in the info file, while the minor and major alleles in the info file were major/minor alleles with respect to the reference panel allele frequency and NOT imputed data allele frequency. As a result, the users only had the <del class="diffchange diffchange-inline">minor allele frequency </del>in their info files but NO way of knowing which one was the minor allele in the imputed data (although most of the times we have the same major/minor <del class="diffchange diffchange-inline">allele in </del>the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5).</div></td><td class='diff-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>['''P.S.''' There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file makes it easier for users to get the minor allele in the imputed data. In the earlier versions, we only reported the minor allele frequency <ins class="diffchange diffchange-inline">(MAF) </ins>of the imputed data in the info file, while the minor and major alleles <ins class="diffchange diffchange-inline">reported </ins>in the info file were major/minor alleles with respect to the reference panel allele frequency and NOT imputed data allele frequency. As a result, the users only had the <ins class="diffchange diffchange-inline">MAF of their imputed data </ins>in their info files but NO way of knowing which one was the minor allele in the imputed data (although most of the times we have the same major/minor <ins class="diffchange diffchange-inline">alleles between </ins>the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5)<ins class="diffchange diffchange-inline">. In the new version, we report the REF and ALT alleles and the ALT allele frequency along with MAF; thus comparing the MAF with the alternate allele frequency, one can easily determine the minor allele in the their imputed data. Please contact [mailto:sayantan@umich.edu Sayantan Das] for any queries we have. We, the authors of Minimac3, apologize for any inconvenience caused due to these updates</ins>.</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;"></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;"></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>= Introduction =</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>= Introduction =</div></td></tr>
</table>Santy.8128http://genome.sph.umich.edu/w/index.php?title=Minimac3_Info_(Older_Version)&diff=13866&oldid=prevSanty.8128 at 17:15, 19 October 20152015-10-19T17:15:46Z<p></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" 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 17:15, 19 October 2015</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>'''If you downloaded Minimac3 version earlier than 0.1.13 (can check the LOG file; source code downloaded before Oct 15, 2015 or imputed data downloaded from Imputation Server) please see this page for Info File descriptors. If using version 0.1.13 or above, please see [[Minimac3 Info File | new version of Minimac3 Info page]]''' !!!</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>'''If you downloaded Minimac3 version earlier than 0.1.13 (can check the LOG file; source code downloaded before Oct 15, 2015 or imputed data downloaded from Imputation Server) please see this page for Info File descriptors. If using version 0.1.13 or above, please see [[Minimac3 Info File | new version of Minimac3 Info page]]''' !!!</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;"></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;"></td></tr>
<tr><td class='diff-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>'''<del class="diffchange diffchange-inline">[</del>P.S There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file makes it easier for users to get the minor allele in the imputed data. In the earlier versions, we only reported the minor allele frequency of the imputed data in the info file, while the minor and major alleles in the info file were major/minor alleles with respect to the reference panel allele frequency and NOT imputed data allele frequency. As a result, the users only had the minor allele frequency in their info files but NO way of knowing which one was the minor allele in the imputed data (although most of the times we have the same major/minor allele in the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5).</div></td><td class='diff-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 class="diffchange diffchange-inline">[</ins>'''P.S<ins class="diffchange diffchange-inline">.''' </ins>There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file makes it easier for users to get the minor allele in the imputed data. In the earlier versions, we only reported the minor allele frequency of the imputed data in the info file, while the minor and major alleles in the info file were major/minor alleles with respect to the reference panel allele frequency and NOT imputed data allele frequency. As a result, the users only had the minor allele frequency in their info files but NO way of knowing which one was the minor allele in the imputed data (although most of the times we have the same major/minor allele in the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5).</div></td></tr>
<tr><td class='diff-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><del class="diffchange diffchange-inline">'''</del></div></td><td class='diff-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 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>= Introduction =</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>= Introduction =</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;"></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;"></td></tr>
</table>Santy.8128http://genome.sph.umich.edu/w/index.php?title=Minimac3_Info_(Older_Version)&diff=13865&oldid=prevSanty.8128 at 17:15, 19 October 20152015-10-19T17:15:26Z<p></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" 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 17:15, 19 October 2015</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>'''If you downloaded Minimac3 version earlier than 0.1.13 (can check the LOG file; source code downloaded before Oct 15, 2015 or imputed data downloaded from Imputation Server) please see this page for Info File descriptors. If using version 0.1.13 or above, please see [[Minimac3 Info File | new version of Minimac3 Info page]]''' !!!</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>'''If you downloaded Minimac3 version earlier than 0.1.13 (can check the LOG file; source code downloaded before Oct 15, 2015 or imputed data downloaded from Imputation Server) please see this page for Info File descriptors. If using version 0.1.13 or above, please see [[Minimac3 Info File | new version of Minimac3 Info page]]''' !!!</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;"></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;"></td></tr>
<tr><td class='diff-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><del class="diffchange diffchange-inline"> </del>'''[P.S There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file makes it easier for users to get the minor allele in the imputed data. In the earlier versions, we only reported the minor allele frequency of the imputed data in the info file, while the minor and major alleles in the info file were major/minor alleles with respect to the reference panel allele frequency and NOT imputed data allele frequency. As a result, the users only had the minor allele frequency in their info files but NO way of knowing which one was the minor allele in the imputed data (although most of the times we have the same major/minor allele in the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5).</div></td><td class='diff-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>'''[P.S There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file makes it easier for users to get the minor allele in the imputed data. In the earlier versions, we only reported the minor allele frequency of the imputed data in the info file, while the minor and major alleles in the info file were major/minor alleles with respect to the reference panel allele frequency and NOT imputed data allele frequency. As a result, the users only had the minor allele frequency in their info files but NO way of knowing which one was the minor allele in the imputed data (although most of the times we have the same major/minor allele in the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5).</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;"><div>'''</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>'''</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;"><div>= Introduction =</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>= Introduction =</div></td></tr>
</table>Santy.8128http://genome.sph.umich.edu/w/index.php?title=Minimac3_Info_(Older_Version)&diff=13864&oldid=prevSanty.8128 at 17:15, 19 October 20152015-10-19T17:15:18Z<p></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" 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 17:15, 19 October 2015</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>'''If you downloaded Minimac3 version earlier than 0.1.13 (can check the LOG file; source code downloaded before Oct 15, 2015 or imputed data downloaded from Imputation Server) please see this page for Info File descriptors. If using version 0.1.13 or above, please see [[Minimac3 Info File | new version of Minimac3 Info page]]''' !!!</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>'''If you downloaded Minimac3 version earlier than 0.1.13 (can check the LOG file; source code downloaded before Oct 15, 2015 or imputed data downloaded from Imputation Server) please see this page for Info File descriptors. If using version 0.1.13 or above, please see [[Minimac3 Info File | new version of Minimac3 Info page]]''' !!!</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;"></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;"></td></tr>
<tr><td class='diff-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><del class="diffchange diffchange-inline"> </del>[There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file makes it easier for users to get the minor allele in the imputed data. In the earlier versions, we only reported the minor allele frequency of the imputed data in the info file, while the minor and major alleles in the info file were major/minor alleles with respect to the reference panel allele frequency and NOT imputed data allele frequency. As a result, the users only had the minor allele frequency in their info files but NO way of knowing which one was the minor allele in the imputed data (although most of the times we have the same major/minor allele in the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5).</div></td><td class='diff-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 class="diffchange diffchange-inline"> '''</ins>[<ins class="diffchange diffchange-inline">P.S </ins>There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file makes it easier for users to get the minor allele in the imputed data. In the earlier versions, we only reported the minor allele frequency of the imputed data in the info file, while the minor and major alleles in the info file were major/minor alleles with respect to the reference panel allele frequency and NOT imputed data allele frequency. As a result, the users only had the minor allele frequency in their info files but NO way of knowing which one was the minor allele in the imputed data (although most of the times we have the same major/minor allele in the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5).</div></td></tr>
<tr><td class='diff-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> </div></td><td class='diff-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 class="diffchange diffchange-inline">'''</ins></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;"><div>= Introduction =</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>= Introduction =</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;"></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;"></td></tr>
</table>Santy.8128