Question: Snprelate And Vcf
gravatar for Adrian Pelin
6.4 years ago by
Adrian Pelin2.4k
Adrian Pelin2.4k wrote:


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 • 2.7k views
ADD COMMENTlink modified 6.4 years ago by zhengxwen0 • written 6.4 years ago by Adrian Pelin2.4k
gravatar for zhengxwen
6.4 years ago by
zhengxwen0 wrote:

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



ADD COMMENTlink written 6.4 years ago by zhengxwen0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1056 users visited in the last hour