Merge 4 bim files by keeping only the overlapping variants (unique rs values )


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# 1  
Merge 4 bim files by keeping only the overlapping variants (unique rs values )

Dear community, I am facing a problem and I kindly ask your help:


I have 4 different data sets consisted from 3 different types of array.



On each file, column 1 is chromosome position, column 2 is SNP id etc... Lets say I have the following (bim) datasets:


x2014:
Code:
1       rs3094315       0       752566  G       A
1       rs3131972       0       752721  G       A

....more 550.000


x2016:
Code:
0       200610-10       0       0       G       A
0       200610-108      0       0       G       A

...


x2017
Code:
0       200610-10       0       0       G       A
0       200610-108      0       0       G       A

...



x2018:
Code:
0       200610-10       0       0       G       A
0       200610-108      0       0       G       A

.....more 550K rows




How can I merge all files together, without having any duplicate values based on the 2nd column (rs_id)?

Last edited by vbe; 01-04-2020 at 12:40 PM.. Reason: code tage please
# 2  
Hi
So your files look like this exactly?
cat file
Code:
x2014:  1       rs3094315       0       752566  G       A
        1       rs3131972       0       752721  G       A
        ...
x2016:  0       200610-10       0       0       G       A
        0       200610-108      0       0       G       A
        ...

or maybe
cat file
Code:
x2014:
1       rs3094315       0       752566  G       A
1       rs3131972       0       752721  G       A       
...     
x2016:
0       200610-10       0       0       G       A
0       200610-108      0       0       G       A       
...

# 3  
Maybe these are file names x2014 x2016 x2017 x2018 ?
Five hundred thousand rows for an array in AWK is a drop in the bucket
Code:
awk '!T[$2]++' x201[4678] > ONE_FILE

# 4  
Thank you for your replies. I know that it may seems easy but I am a beginner with Bash.



@nezabudka



Yes, x2014, x2015 are the file-names! There are like like the 2nd one:
Code:
cat x2014
 1       rs3094315       0       752566  G       A 

1       rs3131972       0       752721  G       A


etc..



Moderator's Comments:
Mod Comment
Please wrap all code, files, input & output/errors in CODE tags.
It makes it easier to read and preserves spacing for indenting or fixed-width data.

Last edited by rbatte1; 01-07-2020 at 01:57 PM..
# 5  
Ok
Then this is what the doctor ordered. The command from the post #3 will filter duplicate values for 2 field.
If you need to select by the unique value of the entire line then so
Code:
awk '!T[$0]++' x201[4678] > ONE_FILE

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