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Top Forums UNIX for Beginners Questions & Answers Merge 4 bim files by keeping only the overlapping variants (unique rs values ) Post 303042724 by fondan on Saturday 4th of January 2020 11:17:26 AM
Old 01-04-2020
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
 

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COMM(1) 							   User Commands							   COMM(1)

NAME
comm - compare two sorted files line by line SYNOPSIS
comm [OPTION]... FILE1 FILE2 DESCRIPTION
Compare sorted files FILE1 and FILE2 line by line. With no options, produce three-column output. Column one contains lines unique to FILE1, column two contains lines unique to FILE2, and column three contains lines common to both files. -1 suppress column 1 (lines unique to FILE1) -2 suppress column 2 (lines unique to FILE2) -3 suppress column 3 (lines that appear in both files) --check-order check that the input is correctly sorted, even if all input lines are pairable --nocheck-order do not check that the input is correctly sorted --output-delimiter=STR separate columns with STR --help display this help and exit --version output version information and exit Note, comparisons honor the rules specified by 'LC_COLLATE'. EXAMPLES
comm -12 file1 file2 Print only lines present in both file1 and file2. comm -3 file1 file2 Print lines in file1 not in file2, and vice versa. GNU coreutils online help: <http://www.gnu.org/software/coreutils/> Report comm translation bugs to <http://translationproject.org/team/> AUTHOR
Written by Richard M. Stallman and David MacKenzie. COPYRIGHT
Copyright (C) 2013 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>. This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. SEE ALSO
join(1), uniq(1) The full documentation for comm is maintained as a Texinfo manual. If the info and comm programs are properly installed at your site, the command info coreutils 'comm invocation' should give you access to the complete manual. GNU coreutils 8.22 June 2014 COMM(1)
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