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Editorial Team
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Asked: 2026-06-15T00:23:15+00:00

I need to create a file from two input files using linux command input

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I need to create a file from two input files using linux command

input 1:

21 33210001 rs60180678 G T 100 PASS AVGPOST=1.0000;RSQ=0.9885;THETA=0.0002;AA=G;AN=2184;VT=SNP;LDAF=0.0019;SNPSOURCE=LOWCOV;AC=4;ERATE=0.0003;AF=0.0018;AFR_AF=0.01 GT:DS:GL

input 2:

21 33210001 . G T . . ;AA=0.0163934;AFE=0;ASNE=0;EUN=0;AFW=0.0113636;MED=0;LAT=0;VT=SNP;AF=0.0018

expected output:

21 33210001 rs60180678 G T . . ;AA=0.0163934;AFE=0;ASNE=0;EUN=0;AFW=0.0113636;MED=0;LAT=0;VT=SNP;AF=0.0018

Each coloumn is separated by tab space.

Creating the output based on 1st,2nd,4th and 5th column match .

Each column of out file is separated by tab space.

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1 Answer

  1. Editorial Team

    Here’s one way with awk:

    awk 'BEGIN { FS=OFS="\t" } FNR==NR { a[$1,$2,$4,$5]=$3; next } ($1,$2,$4,$5) in a { $3=a[$1,$2,$4,$5] }1' file1 file2

    Results:

    21 33210001 rs60180678 G T . . ;AA=0.0163934;AFE=0;ASNE=0;EUN=0;AFW=0.0113636;MED=0;LAT=0;VT=SNP;AF=0.0018
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