PennCNV Command Line Reference

For all Perl programs in PennCNV, you can use both double dash or single dash in the command line (so --output has the same meaning as -output), and you can omit trailing letters of the argument as long as there is no ambiguity with another argument (so the --output argument has the same meaning as the -o or -ou or -out or -outp or -outpu argument).

For each program, the command line options and their explanations can be also viewed by running the program with the -h argument. Furthermore, for each program, the complete manual can be displayed on the screen by running the program with the -m argument.