OK. Well, first use: (a) use strict; (b) use warnings; (c) my variables.

Now, in your input loop you have:

  @t = split(/\t/, $_) ;
  $t[4]= $AB{[4]} ;
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which is a horrible mess :-( What you want to do is:

  $AB{$alpha_numeric_field} = $numeric_field ;
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where the two fields are elements of @t, I cannot tell which.

The output process contains:

  if ($var1[2] and exists $Ab{$var1[2]}) {
    print OUT "$var1[0]\t$var1[1]\t$var1[2]\t$AB[4]\n" ;
  }
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which looks as though it would be OK, but for $AB[4], which ought to be $AB{$var1[2]}. (Oh. And it should be $AB{...} in the if !).

use strict would have picked up the $Ab{} mistake (undefined hash %Ab) and the use of $AB[4] (undefined array @AB). It would not, however, have picked up $AB{[4]}, which is the kind of honest-to-goodness inscrutability that Perl is justly famous for, and which one grows to be deeply fond of.

BTW, rather than:

  @var1 = split(/\t/,$_) ;
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you can write (for example):

  ($field_name, $other_field, $further_field, ...) = split(...) ;
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then you have each field in a variable with a meaningfull name -- more friendly than $var1[2] etc.