Can anyone share me a good GATK4 workflow, I Couldnt find anything good that explanins the process in a crisp and easy way.
is your goal to run it or understand it? ideally both I'm sure but in reality these may be somewhat opposing goals
I don't think you'd find many better resources for GATK4 than those provided by the Broad Institute themselves. Check out the getting started page and the best practices described within.
There are several example scripts online for GATK pipeline. May not be the best, crisp and easy way. Here is GATK workflow for variant calling in RNAseq (https://ssvbio.github.io/rna-seq-and-gatk-best-practices). Probably applicable for WGS and WES for human samples.
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