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Editorial Team
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Asked: 2026-05-31T15:58:30+00:00

I have two files, that look like this: File 1 (2 columns): ID1 123

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I have two files, that look like this:

File 1 (2 columns):

ID1 123
ID2 234
ID3 232
ID4 344
...

File 2 (>1 million columns)

ID2 A C ...
ID3 G T ...
ID1 C T ...
ID4 A C ... 
...

I want to add the values from column 2 of file 1 based on the ID to file 2 as the second column. So the merged file should look like this:

ID2 234 A C ...
ID3 232 G T ...
ID1 123 C T ...
ID4 344 A C ... 
...

So exactly the same as file 2 (same order of rows), but with the added 2nd column. The IDs are the values of the first column (present in both files). File 1 has more rows/IDs than file 2. All IDs from file 2 are in file 1, but not all IDs from file 1 are in file 2.

Does anyone know how to do this under unix/bash? Many thanks!

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1 Answer

  1. Editorial Team
    $ join <(sort file1) <(sort file2)
ID1 123 C T ...
ID2 234 A C ...
ID3 232 G T ...
ID4 344 A C ...

    If you want keep the order of file2

    $ join -1 1 -2 2 <(sort file1) <(cat -n file2 | sort -k2,2) | sort -k3,3n | cut -d' ' -f1-2,4-
ID2 234 A C ...
ID3 232 G T ...
ID1 123 C T ...
ID4 344 A C ...
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