demultiplex mixture of genotyped and non-genotyped samples

[notimenocall]

Hi team,

Thanks for the great tool.

I multiplexed 4 samples with 3 having genotype info and one not, thinking that whatever not matching the existing genotypes will be the non-genotyped donor. I haven't gotten the results from demuxlet yet using the input vcf containing only 3 donor info, but is there a best practice in this scenario or any advice at all? Would you recommend using a genotype-free demultiplexing method here? I am concerned if some cells will be misidentified due to the missing donor genotype.

Thanks much!

Best,
Xiao