use strict;
use warnings;
use List::Util qw/first/;

my @chromosomes = ( "chr1", "chr2", "chr3", "chr5" );
my @line = ( "chr1", "chr3", "chr5" );

if ( grep $line[2] eq $_, @chromosomes ) {
	print "Found $line[2] using grep!\n";
}

if ( first { $line[2] eq $_ } @chromosomes ) {
	print "Found $line[2] using first!\n";
}