How to convert txt or csv files into ped files?

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6.4 years ago

sjunlee89 ▴ 10

I have the information "FID, IID, PID, MID, Sex, Pheno, Genotype1 allele A ...." with csv file.

I would like to convert this file into ped file for analyzing in plink software.

However, I could not find how to conduct this work.

Please let me know how to deal with this problem.

With R, python, or others... anything is fine.

plink ped R python • 7.7k views

ADD COMMENT • link updated 6.2 years ago by zx8754 12k • written 6.4 years ago by sjunlee89 ▴ 10

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What have you tried? From what you're saying, it looks like you can extract pedigree information from the file you have and use it to create a ped, bim and fam file using vcftools/plink.

ADD REPLY • link 6.4 years ago by Ram 44k

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Thank you for your replay. I'm sorry that it was too late... but it had been solved.

ADD REPLY • link 6.2 years ago by sjunlee89 ▴ 10

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Please add the solution as an answer so the question can be marked as solved.

ADD REPLY • link 6.2 years ago by Ram 44k

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You will need to convert that txt/cvs file into ped and map, formats as described in below links:

ADD REPLY • link 6.2 years ago by zx8754 12k

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Thank your for your comment. I'm sorry that it was too late... Fortunately, it had been solved.

ADD REPLY • link 6.2 years ago by sjunlee89 ▴ 10

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