Hi - I'm new to Plink and am trying to read in a transposed fileset so that I can then convert it to bed/bim/fam, but I keep getting this message that says "Note: Variant ####### is triallelic. Setting rarest alleles to missing." Where there are many lines and the ####### ranges from 0-497197. But it still creates files that have the extension .temporary.bed.tmp, .temporary.bim, and .temporary.fam.

So my problem is that I can't figure out why it thinks that they're all triallelic when I can look at my .tfam file and see that they aren't (or at least don't appear so to me). Does anyone have any suggestions?

My tped input looks like this (just with 497198 SNPs):

12    rs1000000    0    126890980    A A    B B    B B    B B
4    rs10000023    0    95733906    B B    B A    B A    B A
4    rs10000030    0    103374154    B B    B B    B B    A B
4    rs10000041    0    165621955    A A    B B    B B    B A
4    rs10000042    0    5237152    B B    B B    B B    B B

My plink command looks like this:

./plink --tfile myfile --recode --out myfile

And the return I get from plink looks like this:

Note: Variant XXXXXX is triallelic.  Setting rarest alleles to missing.

In addition, I'm also getting the error (on the very last line) but I thought the centimorgan position was allowed to be 0?:

Error: Invalid centimorgan position on line 2 of .tped file

Any help would be much appreciated - thanks in advance!