how to determine bacteria relatedness from two variant calls

Question

[Charles Yin]

When the NGS reads of an unknown bacteria are mapped to two reference genomes for variant calls, how do we determine the relatedness the unknown bacteria to each reference genome? From SNPs, assuming mappings fully cover two reference genomes, is there a metric that determines which reference is closer to the unknown bacteria?

Answer 1

[Ian]

You could try SNPRelate (https://bioconductor.org/packages/release/bioc/html/SNPRelate.html). You can create a PCA plot of the samples based on their VCF files.

[Charles Yin]

Thank you very much for your suggestions!