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Extract specific variants from binary plink files

Hi, I have plink binary file (mydata.ped, mydata.fam, and mydata.bim). Using this data I need to create a file that will contain all patients with two APOE variants. Ideally this file willl be in a text format and will contain patients identifier (IID and/or FID) and two APOE variants. However, I do not know how to do it. I will be very grateful for any advice. Many thanks. O

snp gene plink
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updated by kakukeshi kakukeshi • written by OAJn8634 OAJn8634

1 answer

Create a file called, for example, snps.txt with the list of SNPs you want to extract and then run

plink \
 --bed mydata.bed \
 --bim mydata.bim \
 --fam mydata.fam \
 --extract snps.txt \
 --make-bed \
 --out mydata_subset
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updated by zx8754 zx8754 • written by kakukeshi kakukeshi

Hi, Thank you so much for this. It is so helpful. I have just tried to run this and I get the following error:

Error: No variants remaining after --extract.

I am a bit puzzled by this as I have more than 20M variants. I would have thought it would be extremely unlikely if the Apoe variants are not among them. I will be grateful for any thought regarding this.

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written by OAJn8634 OAJn8634

Check using grep in the bim file (chr19)

grep "rs7412" mydata.bim
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updated by zx8754 zx8754 • written by kakukeshi kakukeshi

Hi, Thank you so much for your help. I have checked with grep and the APOE does not appear to be among my variants (even though I have more than 20M of them (imputed)). Is it possible that there is something incorrect with my data?

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written by OAJn8634 OAJn8634

By the way, even when I run this command for a variant that I know is present in my data, I get the same error. Perhaps there is another way of constructing the text format and will contain patients identifier (IID and/or FID) and APOE. Many thanks in advance

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written by OAJn8634 OAJn8634

check in the log if its really reading the variants in the snps.txt file

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written by kakukeshi kakukeshi

It has worked! Thank you so much for your advice and patience :)

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written by OAJn8634 OAJn8634

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