Can I create Mutet2 PON with hg38 instead of hg19?
is there any PON/Mutect workflow that uses the hg38 human genome reference other than hg19 required by these gatk workflows?
My analysis_ready_bam were aligned with hg38 and I was wondering if running panel of normals with hg19 (aka b37) will have any significant impact on other downstream analysis?
Yes, you'll just need to change the workflow attribute configurations to hg38 reference data. You can find hg38 equivalent reference files for mutect2 here: https://console.cloud.google.com/storage/browser/gatk-best-practices/somatic-hg38/
Side note you should use the latest version of the workflow which can be found in the Somatic-SNVs-Indels-GATK4 featured workspace.
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