Question: Input file for MDR(Multifactoral dimension reduction) for exome data
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gravatar for vvividhya93
3.5 years ago by
vvividhya930 wrote:

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

next-gen • 1.1k views
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