Possible to merge three plink bim, bed and fam files?
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7 weeks ago
salman_96 ▴ 30

Hi, I am using plink1.9 and trying to merge three plink binary files. They are all controls.

Test_1.bim Test_1.bed Test_1.fam

Test_2.bim Test_2.bed Test_2.fam

Test_3.bim Test_3.bed Test_3.fam

I am using
plink1.9 --noweb --bfile Test_1 --bmerge Test_2.bim Test_2.bed Test_2.fam Test_3.bim Test_3.bed Test_3.fam --make-bed --out All_controls

I get this error Error: --bmerge accepts at most 3 parameters.

Because I am using 6 parameters. If I use 3 parameters, I may lose some information. Please assist

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7 weeks ago
4galaxy77 ▴ 710

Create a list.txt like

Test_2
Test_3


Then run:

plink --bfile Test_1 --merge-list list.txt --make-bed --out All_controls

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Should the list.txt file have only two of .bim files of all six files. COuld you suggest how do I make it in Linux.

Best regards

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Hi Salman. plink files come in sets of 3. Each set has a .bed, .bim and .fam file. For example, your dataset Test_2 will have a Test_2.bim, Test_2.bed, Test_2.fam file. When you run a plink command, you only need to specify the prefix (i.e. whatever comes before the .bim, .bed or .fam). So you only need a list of prefixes - in this case, just Test_2 and Test_3.

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Hi sorry for the confusion but I did not understand about creating a list.txt file. What would this file have?

I have 3 plink set of files of controls that I want to merge. How do I create list.txt file?

Regards

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All list.txt needs to be is what I posted in the original answer. Did you try and run that? If you are still unsure then read this https://www.cog-genomics.org/plink/1.9/data#merge_list