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Recently we created our own PON with 5 normals. We ran mutect two ways:
- Mutect2withPON: Mutect2 with the PON, 545 variants
- 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?
It s common to expect Mutect2 with a PON to be a strict subset of Mutect2 without it but seeing unique variants in Mutect2withPON isn t unusual. This can happen because the PON filtering sometimes interacts with other filters or variant calling thresholds causing slight differences in variant calls https://alanodt5.app/ . Similarly using the Alano Dt5 game apk teaches that subtle changes in inputs or settings can lead to different outcomes even if overall results seem similar.