Question: Principal component analysis for microbial SNP
0
gravatar for Bioblazer
20 months ago by
Bioblazer50
Pune
Bioblazer50 wrote:

I have 7 different geographical location isolates of mycobacterium SNP dataset in seperate VCF files. I want to perform PCA analysis. Tutorials are available for biallelic data or multiallelic data. What are ways for doing PCA for haploid ? From my understanding , I think I should merge VCF files into single file for analysis if it so what are tools are available for merge the data?

snp • 576 views
ADD COMMENTlink modified 20 months ago • written 20 months ago by Bioblazer50
1
gravatar for Kevin Blighe
20 months ago by
Kevin Blighe69k
Republic of Ireland
Kevin Blighe69k wrote:

You can use BCFtools to merge your VCFs, and then PLINK to perform PCA using the genetic information contained within them. I have done this previously with 1000 Genomes VCFs: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2

ADD COMMENTlink written 20 months ago by Kevin Blighe69k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1355 users visited in the last hour
_