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Editorial Team
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Asked: 2026-06-13T12:19:09+00:00

I have two files I’m trying to join/merge based on columns 1 and 2.

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I have two files I’m trying to join/merge based on columns 1 and 2.

input1

22  42960000    rs149201999 A   AC  100 PASS    LDAF=0.0649;RSQ=0.8652;AN=2184;ERATE=0.0046;VT=SNP;AA=.;AVGPOST=0.9799;THETA=0.0149;SNPSOURCE=LOWCOV;AC=134;AF=0.06;ASN_AF=0.04;AMR_AF=0.05;AFR_AF=0.10;EUR_AF=0.06

input2

22  42960000    .   A   AC  .   .    ;AA=1;AFE=0.989691;ASNE=1;EUN=0.992509;AFW=1;MED=0.991071;LAT=1

And output will be

22  42960000    .   A   AC  .   .    ;AA=1;AFE=0.989691;ASNE=1;EUN=0.992509;AFW=1;MED=0.991071;LAT=1;LDAF=0.0649;RSQ=0.8652;AN=2184;ERATE=0.0046;VT=SNP;AA=.;AVGPOST=0.9799;THETA=0.0149;SNPSOURCE=LOWCOV;AC=134;AF=0.06;ASN_AF=0.04;AMR_AF=0.05;AFR_AF=0.10;EUR_AF=0.06

note each column is separated by tab.

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1 Answer

  1. Editorial Team

    Here’s one way using GNU awk:

    awk 'FNR==NR { array[$1,$2]=$8; next } ($1,$2) in array { print $0 ";" array[$1,$2] }' input1 input2

    Result:

    22  42960000    .   A   AC  .   .    ;AA=1;AFE=0.989691;ASNE=1;EUN=0.992509;AFW=1;MED=0.991071;LAT=1;LDAF=0.0649;RSQ=0.8652;AN=2184;ERATE=0.0046;VT=SNP;AA=.;AVGPOST=0.9799;THETA=0.0149;SNPSOURCE=LOWCOV;AC=134;AF=0.06;ASN_AF=0.04;AMR_AF=0.05;AFR_AF=0.10;EUR_AF=0.06
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