convert.ped- illegal genotype (three alleles)

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dahgam72
Posts: 3
Joined: Wed Nov 23, 2016 9:16 am

convert.ped- illegal genotype (three alleles)

Postby dahgam72 » Wed Nov 23, 2016 9:45 am

Hi,
Please help me with the below problem.

Code: Select all

snp<-convert.snp.tped(ped="snp.ped",mapfile="snp.map",out="genos.raw")
Error: illegal genotype (three alleles) snp 'rs8142331' file 'snp.ped' line 201 !

Thanks in advance
Last edited by lckarssen on Wed Nov 23, 2016 11:25 am, edited 1 time in total.
Reason: Formatted code and output using [code] tags

lckarssen
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Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: convert.ped- illegal genotype (three alleles)

Postby lckarssen » Wed Nov 23, 2016 11:59 am

As the error message says: it seems that you have a triallelic SNP in line 201. Have you verified that line in the tped file?
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Lennart Karssen
PolyOmica
The Netherlands
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dahgam72
Posts: 3
Joined: Wed Nov 23, 2016 9:16 am

Re: convert.ped- illegal genotype (three alleles)

Postby dahgam72 » Wed Nov 23, 2016 12:20 pm

No there are no triallelic SNP in line 201, Actually there is no 201.
The file is not tped file.

dahgam72
Posts: 3
Joined: Wed Nov 23, 2016 9:16 am

Re: convert.ped- illegal genotype (three alleles)

Postby dahgam72 » Wed Nov 23, 2016 1:50 pm

Hi Lennart,

There only 200 lines were in the data. and it is not a tped file.

I have created a txt file with a few SNPs that works good. but when I am trying to create the gaww object:
load.gwaa.data i got the following error
Error in read.table(phenofile, header = TRUE, as.is = TRUE) :
more columns than column names

lckarssen
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Re: convert.ped- illegal genotype (three alleles)

Postby lckarssen » Thu Nov 24, 2016 8:36 am

dahgam72 wrote:The file is not tped file.


I'm a bit confused: the title of the topic mentions convert.ped, the code that you pasted says convert.tped. So, your data is in .ped format. Just to be sure, which function did you use?
-------
Lennart Karssen
PolyOmica
The Netherlands
-------

lckarssen
Site Admin
Site Admin
Posts: 321
Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: convert.ped- illegal genotype (three alleles)

Postby lckarssen » Thu Nov 24, 2016 8:38 am

About the number of lines: did you create the .ped file in Linux and now use GenABEL on Windows or the other way around?

How many lines do you expect in the .ped file? 200 (i.e. 200 samples)?
-------
Lennart Karssen
PolyOmica
The Netherlands
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