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Yes, you can run your own command-line Java program using BTEQ's .os command.
Let's assume that your command-line Java program is named foo.bar.MyProgram and let's assume that it requires a Java classpath of dir1/dir2 and dir3/dir4
Then your .os command in BTEQ would be:
.os java -cp dir1/dir2:dir3/dir4 foo.bar.MyProgram