I have recently shifted from GATK 3 to GATK4. It has changed very much. I figured most of the step but one thing is giving me problem is that how to set temporary directory option in GATK4. I have used this option
export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp with this option
--TMP_DIR ./tmp/. As mentioned in this link But it is giving me this error
A USER ERROR has occurred: 'export' is not a valid command.
Can any one please tell me how to resolve this error.