Remove lines from output in files using awk Post: 302976606

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Top Forums Shell Programming and Scripting Remove lines from output in files using awk Post 302976606 by RudiC on Friday 1st of July 2016 11:51:34 AM

07-01-2016

Registered User

Your spec is (not for the first time) rather misleading. There's NO field that contains GT: 0/0 or 1/1 or 2/2. It is left to the reader's interpretation that field 9 is a sort of description for the next field, and field 10 seems to have the respective values. Your unfit code snippet doesn't help either. It doesn't remove any lines, nor will field 9 ever start with 0, 1, or 2.

And, no logic connection between the TWO files is perceivable. You seem to request a solution for ANY file applicable for your two generic files.

Please be aware that a correct, detailed, and carefully taylored specification will save everybody's time including your's!

For your problem, try

Code:

awk '$NF !~ /^(0\/0|1\/1|2\/2)/' file
20      60056   .       G      A.       35      PASS    DP=25;PF=20;MF=5;MQ=60;SB=0.800 GT:AD:DP:GQ:FL  0/1:12,13:25:99:PASS,PASS

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