How tp Extract SNPs values

Hello

I have two files MaleSNPsList.txt (in which I have a list of SNPs) and MaleSNPsValues.ped (in which I have SNPs values extracted for SNPs). I need to have a data file that looks like this

enter image description here .

In place of tree18, I need snp id i.e rs4558857 which is in list,

enter image description here

and in place of 01-256 I need sample id i.e 6 which is values.ped file

enter image description here

please help

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updated 4.3 years ago by zx8754

• written 4.3 years ago by Raju •

Use --extract mySNPs.txt to subset the SNPs. Then drop columns 2-6 from ped file, and get SNP names from map file for columns.

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written 4.3 years ago by zx8754

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