Use of MAP file with PLINK 1 dosages

Georgii Dolgalev

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Dec 6, 2024, 10:34:35 AMDec 6

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I have a dataset with PLINK 1 dosages and the associated FAM and MAP files. When I try to load the dataset using "plink2 --import-dosage {}.out.dosage.gz --fam {}.out.dosage.fam --map {}.out.dosage.map ..." I get an error "Error: --map must be used with --ped".

However, this contradicts the documentation (https://www.cog-genomics.org/plink/2.0/input#import_dosage), which states that "You may specify a companion .map file with --map".

What is the intended behavior? If I can't use a MAP file with the dosages, how do I load the variant annotation information?

Thanks and best,

Christopher Chang

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Dec 6, 2024, 8:15:24 PMDec 6

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Thanks for reporting this; looks like I broke this in August when adding support for .map/.ped comment lines. Bugfix is posted; let me know if you still see any problems.

Georgii Dolgalev

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Dec 9, 2024, 10:07:18 AMDec 9

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With the new version from 6 December 2024, everything works. Thanks a lot for the quick help!

суббота, 7 декабря 2024 г. в 02:15:24 UTC+1, chrch...@gmail.com:

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