I'm preparing to run assocTestMM (GENESIS) but first need to have a GDS file prepared by snpgdsBED2GDS. I'm working with a nonmodel organism that has 19 autosomes and over 1000 scaffolds which are not assigned to any autosome. Interestingly, my GDS files seem to be capped at 255 scaffolds and everything else is being lumped into scaffold "0". How can I resolve this issue so that I can run GWAS and detect associations on all scaffolds?

snpgdsBED2GDS(bedfile, famfile, bimfile, "gatk_882_WG_genotypes_biallelic_snps_VQSR_0.05maf_bis_pruned_totped_recoded_0.1geno.gds")

Some values of 'snp.chromosome' are invalid (should be finite and >= 1)!
Hint: specifying 'autosome.only=FALSE' in the analysis could avoid detecting chromosome coding.

> max(unique(read.gdsn(index.gdsn(genofile, "snp.chromosome"))))
[1] 255
> min(unique(read.gdsn(index.gdsn(genofile, "snp.chromosome"))))
[1] 0

Please use cvt.chr="char" in snpgdsBED2GDS().

See:

?SNPRelate::snpgdsBED2GDS​