How I make alignment data from vcf file

Question

[BlackHole]

Hello!

I have 50 vcf file with many thousand snp, and number of this snd is different. I want to align Its to use its in gwas analysis

How I make it using plink?

Answer 1

[WouterDeCoster]

Your question really doesn't make sense at all, you probably mixed up quite some terminology. Note that you can convert vcf files directly to plink format, the plink manual is very extensive.

Creating an "alignment" from a vcf is impossible and also not what you need if you want to do GWAS in plink.