IBS/IBD calculation in Plink for haploid organisms

[Masih]

I am trying to run plink GWAS for a non-human haploid organism which has shown to have significant population structure. To correct for this structure, I want to use plink IBS clustering but plink automatically eliminates all non-autosomal chromosome from this analysis resulting in error. 

I was wondering why Plink removes haploid chromosome data for calculation of IBS ( This is not explained in the official webpage of plink) and if I just rename chromosome name to human chromosome 1 and run the IBS analysis, would the results be reliable for stratification correction?

Thanks

[Christopher Chang]

You'd have to interpret the raw numbers a bit differently than usual, but yes, it is reasonable to make plink think the data is diploid just for the purpose of calculating the IBS matrix.