Question: PLINK PROBLEMS: .pre raw file conversions and problems with map files
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gravatar for 170141
3.9 years ago by
1701410
Hong Kong
1701410 wrote:

Hi guys, I am new to gwas and need some help. So I have a good dataset for parkinsons disease, and the case/controls are in the .pre (ACGT format) and .map for all the chromosomes.

First question: in order to run an association test on PLINK, how do I combine all the genotypic data and .map from each chromosomes into one file (just copy and paste consecutively?).

Second: I read some other threads about how to convert .pre files to .ped. Other than downloading another software (MEGA2, cause i'm having trouble using it), is there any other way to make this a usable file?

Third: Linking to the previous question, I tried to just convert the .pre files to .ped by just changing the file extension, PLINK accepted it. However, then the cmd prompt came up with : "ERROR: Problem with MAP file line" and it printed the first line of the MAP :

1         xxx,xxx        rsxxxxxxx      G        C        0.988     0.012      30

Maybe something wrong with the format?

Thanks! Please help!

 

snp plink genome • 1.2k views
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