snpgdsLDpruning filtering all SNPs as non-autosomes. Why?
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
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BioGeorge •
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jezkovt •
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jezkovt •
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Hi, jezkovt. I come across the same questions as you did. Did you figure it out?
OP did not log in for over a year, just that you know.
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/