How To Visualize Multidimensional Scaling For Snps

Question

[elethy86]

Hi,

I have SNPs (500.000) from different individuals and I would like to visualize in a graph how these individuals are distant based on the information of SNPs.

I know that I can use a MDS analysis but I do not know which program I have to use. This is an example of mine input data from GATK (Haplotype caller) in vcf file:

Chr01 2184 T C 148.88  PASS T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T C T - - ./. ./. T T T T T T T T T T T T T T T T T T T - T T T   
Chr01 2548 T A 1106.59 PASS T T T T T A T T T T T T T T T T T T T T T T - T T T T ./. T T - T ./. T - T - T ./. ./. ./. T - T T T - T T T ./. T T T T T T T T T ./. T ./. T
Chr01 2572 T A 1261.20 PASS T T A T T T T T T T T T T T T T T T T T T T - T T T T - T T - T ./. T T T - T ./. ./. ./. T T T T T - T T T ./. T T T T T T T T T ./. T ./. T

Answer 1

[Njoki]

Hi, almost nine years later :) did you find the solution to your question? I also have about 13 million SNPs as a .vcf file and I'd want to do multidimensional scaling. Any help is greatly apprecited.

[4galaxy77]

You probably want to do a PCA. Look up plink2

[Njoki]

Thank you for the response. Indeed, I am doing PCA instead.