convert.snp.illumina

Questions about GenABEL (aka *ABEL) suite of packages
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viniciusjunqueira
Posts: 1
Joined: Thu Jan 05, 2017 5:43 pm

convert.snp.illumina

Postby viniciusjunqueira » Thu Jan 05, 2017 5:49 pm

Hi all,

I created a text file as defined in Appendix A of GenABEL manual, but I keep getting the message

Reading genotypes from file './genotype_illumina.txt' ...
Error in convert.snp.illumina(inf = "./genotype_illumina.txt", out = "./gen0i.raw", :
illegal genotype (three alleles) for SNP 'NC0199888' (line 2)!


Bellow the first three rows of my file

name chr pos strand RADA017 RAFU002 RAFA001
NC0199888 1 100 u AA AA AA
NC0200507 1 100 u AA AA AA
NM0325430 1 800 u BB AA BB

I checked many times if exists some genotyped with three alleles and it not exists.

Suggestions?
Thanks in advance!

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

Re: convert.snp.illumina

Postby lckarssen » Sun Jan 08, 2017 10:36 pm

Did you be any chance create the file on Windows and use it on Linux, or the other way around? This could be the result of the different ways Linux and Windows encode the "end-of-line" character.
If you created the file on Windows and now run on Linux, please use the 'dos2unix' tool to convert the file. In the alternative case, please use "unix2dos'.

Oh, and by the way, the first two markers have the same chromosome and position...
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Lennart Karssen
PolyOmica
The Netherlands
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