Question: Snprelate And Vcf
1
gravatar for Adrian Pelin
5.5 years ago by
Adrian Pelin2.3k
Canada
Adrian Pelin2.3k wrote:

Hello,

I have illumina sequencing for 6 isolates and after mapping them to a reference, I obtain a VCF file for each isolate.

I have previously asked how can I use these VCF files to obtain a phylogenetic tree and was suggested to try the R package SNPRelate. I am a bit new to this, and understand that in using SNPRelate I need to convert my vcf to gds format, after which I need to perform LD pruning. I have tried to look this up in many sources, but still do not understand how SNP clusters can affect my phylogenetic results?

Thank you, Adrian

vcf population • 2.4k views
ADD COMMENTlink modified 5.4 years ago by zhengxwen0 • written 5.5 years ago by Adrian Pelin2.3k
0
gravatar for zhengxwen
5.4 years ago by
zhengxwen0
zhengxwen0 wrote:

It is not necessary to perform LD pruning for phylogenetic analyses, if you try genome-wide variants.

Best,

Xiuwen

ADD COMMENTlink written 5.4 years ago by zhengxwen0
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