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Question: Unable to build GDS with more than 255 scaffolds?
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gravatar for naglemi
11 weeks ago by
naglemi0
naglemi0 wrote:

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

 

 

 

 

ADD COMMENTlink modified 11 weeks ago by zhengx20 • written 11 weeks ago by naglemi0
0
gravatar for zhengx
11 weeks ago by
zhengx20
United States
zhengx20 wrote:

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

See:

?SNPRelate::snpgdsBED2GDS​

ADD COMMENTlink written 11 weeks ago by zhengx20
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