How to get rows with similar values in two different columns using command line?
I think it is easy to do with awk, e.g. see here.
For your example, with your data in file:
%  awk '$2 != $3 {print $0}' file
# outputs
cont100 1128 1125
cont1006 103 19
cont104 895 890
cont1078 43 42
cont1081 727 2

%  awk '$2 == $3 {print $0}' file
# outputs:
cont1005 3642 3642
cont1037 3146 3146
cont1056 934 934
cont1059 1750 1750
cont1072 2577 2577


Note that where you say &quot;similar&quot; I am interpreting that to mean &quot;exactly the same&quot;, because that is the case in your example.