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Can we skip --mind?

Hello,

I merged two datasets (bed bim fam) from different platforms using plink. After QC, the people who merged from a file were all removed.

message :: people removed due to missing genotype data (--mind)

I think this is because of merging two sets from different platforms. If so, how high can we raise --mind? Or can we skip --mind?

Thank you in advance!

snp genome snp gene plink
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updated by chrchang523 chrchang523 • written by khn khn

1 answer

What version of plink are you using? Automatic —mind was turned off ~10 years ago...

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written by chrchang523 chrchang523

I am using plink-1.9-7. Can I just change to --mind 1 just to include all patients merged? One file has 1000 patients, and the other file has 5 patients. --mind 0.1 excluded all the 5 patients from the latter file.

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written by khn khn

That version number doesn’t entirely make sense.

While “—mind 1” would solve your immediate problem, I’d look for a way to get plink reinstalled.

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written by chrchang523 chrchang523

Thank you so much for your response. I will reinstall to see if it changes. Thank you!!

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written by khn khn

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