is the red line sentence right? this confident somatic variants through such steps
@picard_gatk_mj I believe it's correct but feel free to let us know if you find a mistake.
@davidben, Thanks a lot.
but the correct three steps never mentioed the paired(tumor and normal) and PON, these two steps will have nothing to do with confident somatic variants ?
The panel of normals is part of running Mutect2. The normal has to be treated specially because when there is tumor-in-normal contamination you can't automatically reject a variant if there's a bit of evidence for it in the normal.