Question: (Closed) How to convert raw GWAS file to Plink
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gravatar for 170141
4.0 years ago by
1701410
Hong Kong
1701410 wrote:

**Repeat question cause nobody answered last time***

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 gwas • 1.4k views
ADD COMMENTlink written 4.0 years ago by 1701410

Hello 170141!

Please don't post duplicates of existing questions. If no one answered, I'm sorry, but reposting questions is unlikely to garner additional interest.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Daniel Swan13k
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