I am new to human whole exome sequencing data analysis. After I am done with whole exome analysis, I annotate the SNPs using VEP(Variant effector predictor) where I get 3 output files i.e) .vcf .vep.txt .txt Now I want to perform a MDR(Multifactoral Dimension reduction) analysis for all the SNPs. So I got to know that I have to use the .vcf out file which I got from the VEP annotation. But what vcf tool should I use to to convert it into a MDR input file which should have samples in the rows and snps in the column and a class which I will decide?
Sample MDR input file
SNP1 SNP2 ............. SNPn class
sample 1 0 sample 2 1 . 0 . 1 sample n 0