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Delete Chromosome With Plink

Hi everybody ! I am working with PLINK and I would like to supress chromosome X and Y and mitochondrial chromosome before doing the quality control.

Do you have an idea of the command I should put ?

Thanks for your help !

snp
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updated by mc • mc • written by sonalier.nathan • sonalier.nathan

1 answer

With plink2 you should be able to add the flags --chr 1-22 to get chromosomes 1 through 22

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written by mc • mc

"--not-chr X,Y,MT" also works.

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written by chrchang523 chrchang523

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