We are doing QTL analysis in diversity outbred mice using r/qtl2 and have a question regarding removing rare SNP alleles. We have a lower 'n' than ideal but cannot repeat the experiment to add more. In my analysis I have some QTLs with massive effects that aren't significant, which we think is due to one mouse having a particularly low or high phenotype and being the only sample to have the specific allele at that locus. It was recommended to us that we could delete the rare SNPs but we are unsure how. Has anyone done this or know how?