Question: snpgdsLDpruning filtering all SNPs as non-autosomes. Why?
0
gravatar for jezkovt
23 months ago by
jezkovt0
jezkovt0 wrote:

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

snprelate snpgdsldpruning • 843 views
ADD COMMENTlink modified 7 months ago by BioGeorge0 • written 23 months ago by jezkovt0

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

ADD REPLYlink written 7 months ago by BioGeorge0

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

ADD REPLYlink written 7 months ago by ATpoint24k

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/

ADD REPLYlink written 7 months ago by BioGeorge0
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