How can i use combination of both -nct and -nt in GATK?

Question

[mandecent.gupta]

Is there any way to use -nct and -nt both to speed up the computation in GATK pipeline?

[ATpoint]

Hi mandecent.gupta, please stop posting these kind of low-efford one-liner questions. If you seek help, please take the time to put together a proper question that gives some details on what you want to do, where the parameters in your question come from and what you have tried so far. People here are generally happy to help with all kinds of problems, but that requires some motivation in the form of a decent and elaborate question. Looking at your posting history, this has mostly not been the case. For the future, please read and follow How To Ask Good Questions On Technical And Scientific Forums.

Answer 1

[Ram]

If you were to, say, use Google, the first hit on GATK parallelization is this page that literally has the phrase:

There are two options for multi-threading with the GATK, controlled by the arguments -nt and -nct, respectively, which can be combined

Please invest some effort before you ask people for help. It helps your credibility when we can see that you've tried your best. The current situation makes you look lazy.