[GenABEL-dev] a problem of illegal genotype (three alleles)

[Marcin Kierczak]

Dear Chalika,

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:

- 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
- letter case , e.g. you have alleles "A", "T" and "a" in your column
- 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.

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.

Good luck!

Marcin

______________________________________________________________________________

Swedish University of Agricultural Sciences
Department of Clinical Sciences

Mailing address:
Box 7023
SE-75007 Uppsala
Sweden

email: marcin.kierczak at slu.se<mailto:orjan.carlborg at slu.se>
phone: +46 72 516 76 36


web: http://www.computationalgenetics.se<http://www.computationalgenetics.se/>
http://www.kierczak.net

facebook: http://www.facebook.com/pages/Computationalgenetics/174216822622706
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On Mar 28, 2013, at 12:57 PM, Yurii Aulchenko <yurii.aulchenko at gmail.com<mailto:yurii.aulchenko at gmail.com>>
 wrote:

Dear Chalika,

This list is dedicated to the discussion related to the development of the
GenABEL suite and project, but not to the user support.

Therefore I think you question is better suited for the forum.genabel.org<http://forum.genabel.org>.
It is also quite likely that you will find some information answering your
question over there.

best regards,
Yurii

On Thu, Mar 28, 2013 at 10:05 AM, Wangdee, C. <C.Wangdee1 at uu.nl<mailto:C.Wangdee1 at uu.nl>> wrote:

Dear,****

** **

I am working with the data set of GWAS on GenABEL. I found a problem when
I run a command convert.snp.ped.****

The program said “Error in convert.snp.ped("pedin1.txt", "map.txt",
"genokooi.raw") : ****

 illegal genotype (three alleles) snp 'BICF2G630100019' file 'pedin1.txt'
line 91 !”****

I tried to manage and get new pedin but the problem cannot solve.****

Could you please help me on this problem?****

** **

Best regards,****

Chalika****

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