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Compare & subtract lines in files by column using awk.

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http://www.unix.com – I have two files with similar column pattern as given below : 2 sample lines from file1 are given below. Code: 18    12630    .    G  T    49.97    .    AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=60.00;MQ0=0;NDA=1;QD=16.66;SB=-0.01    GT:AD:DP:GQ:PL    1/1:0,3:3:9.01:82,9,0 18    12842    .    G    A    82.02    .    AC=1;AF=0.50;AN=2;BaseQRankSum=-1.898;DP=16;Dels=0.00;FS=6.560;HRun=3;HaplotypeScore=3 (HowTos)