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Annotation Exercise - Revision history
2026-04-05T18:30:31Z
Revision history for this page on the wiki
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Serveradmin: /* Annotation exercise */
2017-03-02T16:55:54Z
<p><span dir="auto"><span class="autocomment">Annotation exercise</span></span></p>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 16:55, 2 March 2017</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==Annotation exercise==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==Annotation exercise==</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; 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:black; 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"> mkdir APOC3</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; 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"> cd APOC3</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>  vtools init APOC3</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>  vtools init APOC3</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>  vtools import ../data/APOC3.vcf --format ../data/vcf.fmt --build hg19</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>  vtools import ../data/APOC3.vcf --format ../data/vcf.fmt --build hg19</div></td></tr>
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Serveradmin
http://statgen.us/index.php?title=Annotation_Exercise&diff=262&oldid=prev
Serveradmin: Created page with "__NOTITLE__ ==Annotation exercise== vtools init APOC3 vtools import ../data/APOC3.vcf --format ../data/vcf.fmt --build hg19 vtools select variant --count vtools use refG..."
2017-02-23T18:48:29Z
<p>Created page with "__NOTITLE__ ==Annotation exercise== vtools init APOC3 vtools import ../data/APOC3.vcf --format ../data/vcf.fmt --build hg19 vtools select variant --count vtools use refG..."</p>
<p><b>New page</b></p><div>__NOTITLE__<br />
<br />
==Annotation exercise==<br />
<br />
vtools init APOC3<br />
vtools import ../data/APOC3.vcf --format ../data/vcf.fmt --build hg19<br />
vtools select variant --count<br />
vtools use refGene<br />
vtools show fields<br />
vtools select variant --output chr pos ref alt refGene.name2<br />
vtools use ../data/dbNSFP.DB<br />
vtools show fields<br />
vtools select variant 'id="rs76353203" or id="rs140621530" or id="rs147210663" or id="rs121918381" or id="rs121918382"' -t 5var<br />
vtools select 5var --output chr pos ref alt id dbNSFP.GERP_RS dbNSFP.phyloP100way_vertebrate dbNSFP.phastCons100way_vertebrate<br />
vtools select 5var --output chr pos ref alt dbNSFP.FATHMM_pred dbNSFP.FATHMM_score<br />
vtools select 5var --output chr pos ref alt dbNSFP.Polyphen2_HDIV_pred dbNSFP.Polyphen2_HDIV_score dbNSFP.Polyphen2_HVAR_pred dbNSFP.Polyphen2_HVAR_score<br />
vtools select 5var --output chr pos ref alt dbNSFP.LRT_pred dbNSFP.LRT_score<br />
vtools select 5var --output chr pos ref alt dbNSFP.MutationTaster_pred<br />
vtools select 5var --output chr pos ref alt dbNSFP.PROVEAN_pred dbNSFP.PROVEAN_score<br />
vtools select 5var --output chr pos ref alt dbNSFP.SIFT_pred dbNSFP.SIFT_score<br />
vtools select 5var --output chr pos ref alt dbNSFP.CADD_raw dbNSFP.CADD_phred</div>
Serveradmin