Is there any difference between analyzing the WES and WGS data via GATK best practice?

Question

[Mohamad]

Dear all,

I analyzed WES fastq raw data bt GATK best practice command line and have the complete command lines for it. Now, I want to analyze the WGS data. Can I use the same command line for WGS? If not, could you please tell me the differences in the analysis?

Thanks