Hi haukex, Thanks very much, works perfectly now. I went with

 next if ($chromosome =~ "chrM");

I was using both Strict and Warnings and using the quotes instead of the regex doesn't produce any warnings :D

My apologies about the input data format

Cheers

In reply to Re^2: Trouble skipping lines using Perl by LeBran
in thread Trouble skipping lines using Perl by LeBran

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