Error: tped file has a half-missing call.

Shirley ZHANG

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Apr 27, 2022, 9:03:04 AM4/27/22

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Hi all,

I am trying to use plink --tped file.tped --tfam file.tfam --make-bed --out newName to convert tped and tfam files to binary files. It came with this bug:

Screenshot 2022-04-27 at 13.25.47.png

Here is my tped.file:

Screenshot 2022-04-27 at 13.59.38.png

My tfam.file:

Screenshot 2022-04-27 at 11.26.58.png

Does anyone know how to solve this? Thanks.

Shuya

Christopher Chang

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Apr 27, 2022, 9:23:01 AM4/27/22

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This is not a plink "bug". Your .tped file violates the specification, and you need to fix the problem with whatever generated it.

Christopher Chang

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Apr 27, 2022, 9:27:08 AM4/27/22

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(From the "haploid" in the filename, I am guessing that the program that generated the malformed .tped file incorrectly assumed that it would be okay to include each allele code only once. If so, this would be fixed by duplicating every allele code.)

Shirley ZHANG

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Apr 27, 2022, 10:38:13 AM4/27/22

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Thank you, Christopher! I will have a try (duplicate every allele code.) to see if I can fix the problem.

Shuya

Shirley ZHANG

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Apr 27, 2022, 2:42:48 PM4/27/22

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It works! Cheers

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