Recently we created our own PON with 5 normals. We ran mutect two ways:

1. Mutect2withPON: Mutect2 with the PON, 545 variants
2. Mutect2withoutPON: Mutect2 without the PON, 540 variants

We were assuming, perhaps naively, that Mutect2withPON would be contained in Mutect2withoutPON, and the ones that were missing we would consider results of artifacts that were filtered by the PON.

Indeed, Mutect2withoutPON has 4 variants that Mutect2withPON does not have, presumably those come from artifacts present in the PON. However, Mutect2withPON has 9 variants that Mutect2withoutPON does not have. Does this make sense or are we missing something? Why is this?