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<title>Tagger: Selection and evaluation of tag SNPs</title>

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<div id="breadcrumbs">
<a href="/index.html">Home</a> &gt; <a href="/mpg">Medical &amp; Population Genetics</a> &gt; <a href="/mpg/tagger/">Tagger</a> &gt; Server</div>
<div id="content">

<h1>Tagger</h1>

<form name="thisform" action="submit_tag_request.php" method="POST" enctype="multipart/form-data" onsubmit="return IsEmailValid('thisform','email');">

<table width=100%>
<tr>
<th align=left>your email address (required)</th>
<td><input type=text name="email" maxlength=100 size=50></td>
<td align=center><input type=reset name=reset value="reset" class="buttonReset"></td>
<td align=center><input type=submit name=submit value="submit" class="buttonSubmit"></td>
</tr>
<tr>
<th align=left>description of this run</th>
<td><input type=text name="description" maxlength=100 size=50></td>
</tr>
</table>

<p>
<input type="radio" name="type" onClick="ShowMenu(1)" checked> I want to specify chromosomal landmarks and use a local copy of the HapMap<br>
<input type="radio" name="type" onClick="ShowMenu(2)"> I want to upload a HapMap genotype file<br>
<input type="radio" name="type" onClick="ShowMenu(3)"> I want to upload my own genotype data as a PED file<br>
<input type="radio" name="type" onClick="ShowMenu(4)"> I want to upload my own genotype data which is phased and in Nick Patterson format
</p>

<table width="100%" class="fancy">
<tbody id="1" style="display: ;" colspan="2">
<tr><th colspan=2>chromosomal landmarks</th></tr>
<tr>
<td width="50%">Enter the genomic regions that you want to tag<br>using NCBI Build 35/UCSC hg17/May 2004 coordinates<br>
Example: <b>chr10:114,700,200..114,916,057</b><br>
<textarea name="landmarks" rows=6 cols=40></textarea></td>
<td width="50%">HapMap analysis panel: 
<select name="hapmap_pop">
<option>YRI
<option selected>CEU
<option>CHB+JPT
</select>
<br><br>This uses the phased <a href="http://www.hapmap.org/">HapMap Release 21</a> (incl. chrX)<br><br>
YRI: 2,937,220 polymorphic SNPs<br>
CEU: 2,623,164 polymorphic SNPs<br>
CHB+JPT: 2,480,469 polymorphic SNPs
</td>
</tr>
</tbody>

<tbody id="2" style="display: none;">
<tr><th colspan=2>HapMap genotype dump</th></tr>
<tr>
<td width="50%"><input type=file name="panel_hapmap"></td>
<td width="50%">population sample:
<input type=radio name="pop" value="YRICEU" checked>YRI or CEU 
<input type=radio name="pop" value="CHBJPT">CHB or JPT</td>
</tr>
</tbody>

<tbody id="3" style="display: none;">
<tr>
<th width="50%">linkage format (&quot;ped&quot; file)</th>
<th width="50%">SNP information file</th>
</tr>
<tr>
<td><input type=file name="panel_ped">
<p>this &quot;ped&quot; file contains genotypes, starting at column 
<select name="colstart">
<option>2
<option>3
<option>4
<option>5
<option>6
<option>7
<option selected>8</select>
, of:<br>
<input type=radio name="ped_type" value="cc" checked>unrelated individuals<br>
<input type=radio name="ped_type" value="ped">related individuals (pedigrees)</td>
<td><input type=file name="info_file_ped" size="40"></td>
</tr>
</tbody>


<tbody id="4" style="display: none;">
<tr>
<th width="50%">Nick Patterson format (for phased data)</th>
<th width="50%">SNP information file</th>
</tr>
<tr>
<td width="50%"><input type=file name="panel_emppp"></td>
<td width="50%"><input type=file name="info_file_emppp" size="40"></td>
</tr>
</tbody>

<tr><th colspan=2>SNP design scores (for preferential SNP picking)</th></tr>
<tr>
<td width="50%"><input type=file name="design_scores_file" size="20"></td>
<td width="50%">default design scores for all SNPs: 
<select name="default_design_score">
<option selected>1.0
<option>0.9
<option>0.8
<option>0.7
<option>0.6
<option>0.5
<option>0.4
<option>0.3
<option>0.2
<option>0.1
<option>0.0</select></td></tr>

<tr>
<th>include tag SNPs</th>
<th>exclude tag SNPs</th>
</tr>
<tr>
<td><input type=file name="include_tags"></td>
<td><input type=file name="exclude_tags"></td>
</tr>
<tr>
<td><textarea name="include_tags_contents" rows="4" cols="30"></textarea></td>
<td><textarea name="exclude_tags_contents" rows="4" cols="30"></textarea></td>
</tr>
<tr>
<td><input type=checkbox name="only_evaluate_tags">&nbsp;only evaluate these SNPs (do <b>not</b> pick extra tags)</td>
<td>exclude all SNPs with design scores &lt;
<select name="design_score_threshold">
<option>1.0
<option>0.9
<option>0.8
<option>0.7
<option>0.6
<option>0.5
<option>0.4
<option>0.3
<option>0.2
<option>0.1
<option selected>0.0</select></td>
</tr>

<tr>
<th>which alleles do you want to capture?</th>
<th>minimum allele frequency</th>
</tr>
<tr>
<td><input type=radio name="which_alleles" value="snps" checked>&nbsp;all SNPs (above frequency threshold)
<br><input type=radio name="which_alleles" value="specified">&nbsp;only these specified alleles:
<!--<td><input type=file name="alleles" size="40"></td>--->
<br><textarea name="alleles_contents" rows="3" cols="30"></textarea></td>
<td>
for SNPs:
<select name="min_maf">
<option>0%
<option>1%
<option>2%
<option>3%
<option>4%
<option selected>5%
<option>10%
<option>20%
<option>25%</select><br>
for haplotypes (if you specified any):
<select name="min_haplotype_freq">
<option>2%
<option>3%
<option>4%
<option selected>5%
<option>10%
<option>20%
<option>25%</select>
</td>
</tr>

<tr>
<th>Tagger mode</th>
<th><i>r</i><sup>2</sup> threshold</th>
</tr>
<tr>
<td>
<input type=radio name="tagging_mode" value="pairwise" checked>&nbsp;pairwise<br>
<input type=radio name="tagging_mode" value="aggressive">&nbsp;aggressive (specified multimarker tests)
</td>
<td>for SNPs:
<select name="r2s_cutoff">
<option selected>1.0
<option>0.9
<option>0.8
<option>0.7
<option>0.6
<option>0.5</select>
<br>for haplotypes (if you specified any):
<select name="r2h_cutoff">
<option selected>1.0
<option>0.9
<option>0.8
<option>0.7
<option>0.6
<option>0.5</select></td>
</tr>

<tr><th colspan="2" align="right"><input type=submit name=submit value="submit" class="buttonSubmit"></th></tr>

<tr><th colspan="2">advanced settings</th></tr>
<tr>
<td>maximum number of markers in haplotype tests:
<select name="n_aggressive_markers">
<option>2
<option selected>3
<option>4
<option>5
<option>6</select>
<br>
LOD score threshold:
<select name="lodscore_threshold">
<option>0
<option>1
<option selected>2
<option>3
<option>4
<option>5</select>
<br>
maximum number of tries:
<select name="max_tests">
<option>1000
<option selected>10000
<option>100000
<option>1000000</select>
</td>
<td>maximum tagging distance:
<select name="maximum_tagging_distance">
<option>50 kb
<option>100 kb
<option selected>200 kb
<option>500 kb
<option>1000 kb
<option>2000 kb
<option>5000 kb
<option>10000 kb
<option>20000 kb
<option>50000 kb
<option>100000 kb</select>
<br>
<input type=checkbox name="enable_take_n_best_tags">&nbsp;pick only the <i>N</i> best tags&nbsp;
<input type=text name="take_n_best_tags" size="8" maxlength="5">
<br>
minimum distance between tags:
<select name="min_dist_between_tags">
<option>0
<option>60</select>&nbsp;base pairs
</td>
</tr>

</table>

</form>

<h2>Reference</h2>
<p>P.I.W. de Bakker, R. Yelensky, I. Pe'er, S.B. Gabriel, M.J. Daly, D. Altshuler (2005) Efficiency and power in genetic association studies. <i>Nature Genetics</i>. <b>37</b>: 1217-1223</p>

<h2>Any questions?</h2>
<p>You can contact us at <a href="mailto:tagger@broad.mit.edu">tagger@broad.mit.edu</a>.</p>

</div>

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