my %genotype;
while(<GENOTYPE>) {
	$genotype{$1} = $2 if (/(\d+)\t\w\t(\w)/);
}

while (<REF>) {
	next unless (/(\d+)\t(\w)/); 
	print OUT (defined($genotype{$1}) and ($genotype ne '')) ? "$1\t$genotype{$1}\n" : "$1\t$2\n";
}