I'm trying to use GenABEL and when attemping to use the command;
convert.snp.tped(tpedfile="plink.tped", tfamfile="plink.tfam", out="tdata.dat")
I get the error:
Error in convert.snp.tped(tpedfile = "plink.tped", tfamfile = "plink.tfam", :
illegal genotype (three alleles) snp 'chr1_2367259_D' file 'plink.tped' line 42 !
So I checked the tped file and on line 42 I have:
1 chr1_2367259_D 0 2367259 I2 I2 I2 I2 I2 I2 I2 I2 I2 I2 D I2 I2 I2 I2 I2 I2 I2....
Anyone have experience with this error ? What might have caused the plink conversion to give this output ?
I changed your post to a question because that's what it is and I added genabel and plink to the tags, because those are quite relevant for your problem.
Did you get the plink file from a vcf file? How does the variant look like there?
Unfortunately no vcf file the only plink files I have are .bed .bim .fam
Well, the error is quite clear, no?
illegal genotype (three alleles)
Which alleles does that line contain? I see an
I2
andD
, but likely also anI1
?