Hi! I am performing variant calling starting from a fasta resulting targeted sequencing of ~320 cancer genes, I followed the GATK best practices aligning with the GrCh38 reference.

For the Apply Base Quality Score Recalibration, which files should I use for the "--known-sites" given that i am doing somatic variant calling from targeted sequencing with NO panel of normals.

https://gatk.broadinstitute.org/hc/en-us/community/posts/360075305092-Known-Sites-for-BQSR - This post referes only to WGS/WES not Targeted Sequencing.

 gatk BaseRecalibratorSpark \
   -I $INPUT \
   -R $GENOME \
   --known-sites 
   -O $RECALL 

Thank you! Best Regards.