GWAS Studies

How to create a .ped file for use in PLink? I have the following csv file:

Chromosome Position Sample1 Sample 2 ........... Sample n

Chr                 Pos          Sam1       Sam2     Sam3, Sam 4, ......Sample_n 
1                   11            A          T          T, A, A, T, ......
2                   141           G          G          G, T, T, G, ......

So each row contains the information for nucleotide base for all samples for specific gene locus. I have another file that has information about Phenotype scores for each sample. My only question is how can I generate a .ped file from my inputs to do GWAS analysis?

gwas plink

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written 4.8 years ago by 123 •

are you sure your file contains both a tab / space and comma as a separator? This seems highly unlikely and ill-formed. Maybe show us what your original file look like?

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written 4.8 years ago by Sam

Yes the file is comma separated.

Chr, Pos, Sam1, Sam2, Sam3 ..................... Samn 1, 11, A, T, T ................. 2, 141, G, G, C ....................

Just like that.

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written 4.8 years ago by 123 •

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