Katie,
Could you let me know what version of fastlmm are you using and what host OS? That helps me to better understand the context of any questions coming in.
The PLINK docs say to encode the snp should have both alleles encoded or no alleles encoded. If you are on the x chromosome or y chromosome without a pair, they suggest coding as homozygous rather than missing. In this case, I would expect the SNP to be encoded as [T] [T] or [0] [0].
We usually fix the input so we know what data is being operated on in an attempt to avoid surprises.
I don’t believe there is a switch to fixup or ignore the input we think is suspect.
Thanks
-bobd-