Using SNPRelate for bacteria genomes?

[sofiany]

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Hi! I would love to use SNPRelate for SNPdata from bacteria. Any ideas how I need to modify the vcf file (or R-script) to make it work? In my vcf I only have one column per sample (ex. for E. coli one chromosome /one allele).

All the best /Sofia

[zhengxwen]

Try snpgdsVCF2GDS() in the SNPRelate.