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zhengxwen / SNPRelate

R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)
http://www.bioconductor.org/packages/SNPRelate
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Using SNPRelate for bacteria genomes? #46

Open sofiany opened 6 years ago

sofiany commented 6 years ago

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 commented 6 years ago

Try snpgdsVCF2GDS() in the SNPRelate.