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Dear Chalika,
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<div>this is a common problem -- often it is caused by some weird character in ped file which makes GenABEL think that there are more than two alleles. Often this is caused by:</div>
<div><br>
</div>
<div>- you do not have 6 columns in front of the first genotype column in your file and GenABEL takes phenotype column as the first genotype</div>
<div>- letter case , e.g. you have alleles "A", "T" and "a" in your column</div>
<div>- often it is white-character-related issue, i.e. you have mixed tabs and spaces in your file. This is the most difficult to spot but also the most common thing. It is often caused by the fact that white characters are differently encoded and interpreted
by different OS. If you are using Linux machine and your file was created by a Windows program, it may result in such error.</div>
<div><br>
</div>
<div>I think it would be a tremendous help if GenABEL printed these three alleles and I suppose it is a very easy add-on for one of the next releases.</div>
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</div>
<div>Good luck!</div>
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<div><span class="Apple-tab-span" style="white-space:pre"></span>Marcin<br>
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______________________________________________________________________________</div>
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<div>Swedish University of Agricultural Sciences</div>
<div>Department of Clinical Sciences</div>
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<div>Mailing address:</div>
<div>Box 7023</div>
<div>SE-75007 Uppsala</div>
<div>Sweden</div>
<div><br>
</div>
<div>email: <a href="mailto:orjan.carlborg@slu.se">marcin.kierczak@slu.se</a></div>
<div>phone: +46 72 516 76 36</div>
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</div>
<div><br>
</div>
<div>web: <a href="http://www.computationalgenetics.se/">http://www.computationalgenetics.se</a></div>
<div><a href="http://www.kierczak.net">http://www.kierczak.net</a></div>
<div><br>
</div>
<div>facebook: <a href="http://www.facebook.com/pages/Computationalgenetics/174216822622706">http://www.facebook.com/pages/Computationalgenetics/174216822622706</a></div>
<div>______________________________________________________________________________</div>
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<div>On Mar 28, 2013, at 12:57 PM, Yurii Aulchenko <<a href="mailto:yurii.aulchenko@gmail.com">yurii.aulchenko@gmail.com</a>></div>
<div> wrote:</div>
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<blockquote type="cite">Dear Chalika,<br>
<br>
This list is dedicated to the discussion related to the development of the<br>
GenABEL suite and project, but not to the user support.<br>
<br>
Therefore I think you question is better suited for the <a href="http://forum.genabel.org">
forum.genabel.org</a>.<br>
It is also quite likely that you will find some information answering your<br>
question over there.<br>
<br>
best regards,<br>
Yurii<br>
<br>
On Thu, Mar 28, 2013 at 10:05 AM, Wangdee, C. <<a href="mailto:C.Wangdee1@uu.nl">C.Wangdee1@uu.nl</a>> wrote:<br>
<br>
<blockquote type="cite">Dear,****<br>
<br>
** **<br>
<br>
I am working with the data set of GWAS on GenABEL. I found a problem when<br>
I run a command convert.snp.ped.****<br>
<br>
The program said “Error in convert.snp.ped("pedin1.txt", "map.txt",<br>
"genokooi.raw") : ****<br>
<br>
illegal genotype (three alleles) snp 'BICF2G630100019' file 'pedin1.txt'<br>
line 91 !”****<br>
<br>
I tried to manage and get new pedin but the problem cannot solve.****<br>
<br>
Could you please help me on this problem?****<br>
<br>
** **<br>
<br>
Best regards,****<br>
<br>
Chalika****<br>
<br>
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<br>
</blockquote>
<br>
<br>
<br>
-- <br>
-----------------------------------------------------<br>
Yurii S. Aulchenko<br>
<br>
[ LinkedIn <<a href="http://nl.linkedin.com/in/yuriiaulchenko">http://nl.linkedin.com/in/yuriiaulchenko</a>> ] [<br>
Twitter<<a href="http://twitter.com/YuriiAulchenko">http://twitter.com/YuriiAulchenko</a>>] [<br>
Blog <<a href="http://yurii-aulchenko.blogspot.nl/">http://yurii-aulchenko.blogspot.nl/</a>> ]<br>
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