snpgdsLDpruning filtering all SNPs as non-autosomes. Why?

Question

[jezkovt]

I have SNP data assembled denovo (that is, no chromosomal information available). I converted a vcf file generated using vcftools to GDS using snpgdsVCF2GDS function in the SNPRelate package. However, when I try to analyze the data, all my SNPs are filtered out as non-autosomes. Why is that and how can I fix it?

Thanks so much,

Tereza

[BioGeorge]

Hi, jezkovt. I come across the same questions as you did. Did you figure it out?

[ATpoint]

OP did not log in for over a year, just that you know.

[BioGeorge]

Thanks. I didn't notice that before. And I found one solution for it from the Bioconductor. When using the SNPRelate, adding the autosome.only=FALSE can solve that. https://support.bioconductor.org/p/114050/