Good day,

I'm trying to recreate pipeline that was described in Bioinformatics Analysis of Whole Exome Sequencing Data and i'm facing some problems. Searching for answers i came across various posts, but almost everything is related to either with tumor variants or with Panel of Normals (which i don't have as pipeline only about to be used in the future and only 1 sample of WES available right now).

Is there a way to do variant calling with normal sample without PON ? I'm trying to use Mutect2 as the papers and posts suggest, but encountering various problems and errors, mostly related to interval list and/or lack of tumor/PON samples.