I had some questions about the pre-made panel of normals (PON) files in the Google Cloud Best Practices folder (https://console.cloud.google.com/storage/browser/gatk-best-practices/). It would be great if some documentation regarding these files could be provided.
Specifically, would it be possible to clarify the difference between:
"Mutect2-WGS-panel-b37.vcf" and "Mutect2-exome-panel.vcf" are these files both panel of normal files for use in Mutect2?
Additionally, in the "somatic-hg38" folder there are files titled "1000g_pon.hg38.vcf" and "af-only-gnomad.hg38.vcf". Are these files also panel of normals files for use in Mutect? Would it be possible to describe information these files contain (information from exomes or genomes, etc)? Additionally, I noticed that there does not appear to be an equivalent of the "Mutect2-WGS-panel-b37.vcf" for the hg38 genome build. Is it currently possible to run these analyses using hg38?
Any advice would be greatly appreciated!
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