Yes, open did it, thank you for the suggestion! Here is the code that worked: 
open(GERMS, "| $germline") || die "Could not call germline!\n";
print GERMS "1\n";
print GERMS "$map\n";
print GERMS "$ped\n";
print GERMS "out";
close GERMS;

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In reply to Re^2: Calling and interacting with external executable by verity
in thread Calling and interacting with external executable by verity

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