Recurrent error in data

[Chunkz616]

There is a recurrent rearrangement found in all my calls for the DUX4 unknown partner. Is this a known false positive or am I misunderstanding something? Has this been found before?

[martimij]

This region on chr2 is repetitive (short tandem repeats), so any reads mapping there are less reliable. If this is a recurrent call found in 2+ unrelated samples, then it's safe to assume it's a false positive. We recommend creating a blacklist of recurrent false positives and feeding that to Pelops, as described in the documentation.

[Chunkz616]

Thank you, this makes sense