GATK4 pipeline in easy bash scripts, please
Hi, I asked this question a while ago and a few times. I know, there is a wonderful WDL platform and fire cloud stuff to run things in parallel and check this and that. But, for someone who are so used to a series of simple BASH commands, can you guys please kindly provide an example script like the one shown here https://gencore.bio.nyu.edu/variant-calling-pipeline/?
Right after I found the above, I found that it is not updated with GATK4, and I would hate to use a pipeline that is based on an outdated version of engine.
I will say "Thank You So Much, GATK". For almost a year, I still could not make GATK run on my own server, although there are a million documentation and tutorial and PPTs googled everywhere.