http://genome.sph.umich.edu/w/index.php?action=history&feed=atom&title=Ligate_Minimac 2026-09-25T05:32:38Z Revision history for this page on the wiki MediaWiki 1.43.1 http://genome.sph.umich.edu/w/index.php?title=Ligate_Minimac&diff=8620&oldid=prev 2013-09-10T19:06:39Z

<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 15:06, 10 September 2013</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l45">Line 45:</td> <td colspan="2" class="diff-lineno">Line 45:</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>&lt;/pre&gt;</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>&lt;/pre&gt;</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>Contact welchr@umich.edu for questions/issues.</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>Contact <ins style="font-weight: bold; text-decoration: none;">[mailto:</ins>welchr@umich.edu <ins style="font-weight: bold; text-decoration: none;">welchr@umich.edu] </ins>for questions/issues.</div></td></tr> </table>

Welchr http://genome.sph.umich.edu/w/index.php?title=Ligate_Minimac&diff=8619&oldid=prev 2013-09-10T19:04:57Z

<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 15:04, 10 September 2013</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l44">Line 44:</td> <td colspan="2" class="diff-lineno">Line 44:</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"></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>&lt;/pre&gt;</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>&lt;/pre&gt;</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;">Contact welchr@umich.edu for questions/issues.</ins></div></td></tr> </table>

Welchr http://genome.sph.umich.edu/w/index.php?title=Ligate_Minimac&diff=8616&oldid=prev 2013-09-10T19:02:24Z

<p>Created page with &quot;A script to ligate together chunks created by minimac: [http://csg.sph.umich.edu/boehnke/ligate_minimac/ligate_minimac.py ligate_minimac.py] Usage instructions (can also ru...&quot;</p> <p><b>New page</b></p><div>A script to ligate together chunks created by minimac: <br /> <br /> [http://csg.sph.umich.edu/boehnke/ligate_minimac/ligate_minimac.py ligate_minimac.py]<br /> <br /> Usage instructions (can also run the script without arguments, or with -h): <br /> <br /> &lt;pre&gt;<br /> Usage: ligate_minimac.py -o output_prefix &lt;info files&gt;<br /> <br /> This script assumes the following:<br /> <br /> 1) You are attempting to merge only minimac chunks from the same chromosome<br /> <br /> 2) Dosage files and info files end in .dose (or .dose.gz) and .info (or .info.gz)<br /> <br /> i.e. chr9.1.10000.info.gz and chr9.1.10000.dose.gz<br /> <br /> 3) Markers within info files are sorted by genomic position<br /> <br /> 4) Minimac chunks are disjoint, that is, their markers do not overlap<br /> <br /> You must also have the Unix tools join, cut, gzip/gunzip, tail, sort, and cut.<br /> Additionally, the bash shell must be present on your system; you do not need to<br /> be inside a bash shell to run the script, however.<br /> <br /> The script will not work under Windows.<br /> <br /> Only testing has been done with Python 2.7. Earlier versions of python should<br /> work, but 2.6+ is probably best.<br /> <br /> This script makes heavy use of multiple concurrent processes piped together.<br /> Therefore, you should likely only run 1 job at a time on the same machine.<br /> <br /> Example:<br /> <br /> ./ligate_minimac.py -o my_merged_results chr9*info.gz<br /> <br /> <br /> <br /> Options:<br /> -h, --help show this help message and exit<br /> -o OUT, --out=OUT Output file prefix (files OUT.dose.gz and OUT.info.gz<br /> will be created)<br /> <br /> &lt;/pre&gt;</div>

Welchr