3.2 years ago by
Hi @ reza
I think it would benefit you more if you could use the GATK pipeline.
best practices and then go through the workflow-documentation. Also, remember GATK is an empirical method designed with human genome in mind. But, you may need to deviate from the pipeline in terms of parameters and steps, depending upon what your goal is. Also, remember to read the discussion, Q/A and comments to do what you need to do.
Using a empirical pipeline gives you some easiness, but at the same time everyone has different goals; so results you get should be looked with scrutiny - I mean you need to doubt your results you get using empirical pipelines - in biology and genetics anything can happen; that's the main point of doing biology and using bioinformatics.