Investigating a weird mutation calling artefact I found that a considerable fraction of those artefacts (20-30%, very rough estimate) have certain similarities in their coordinates/tiles. We are using a conservative threshold of 2500 pixels to flag optical duplicates out of NovaSeq S4 flow cells. The following examples are further than 2500 pixels, but they show striking similarities (only showing lane:tile:x:y). The separation of 1000 in tile numbers is very frequent... update: just read that the thousand digit (1 or 2) indicates whether it is "top" or "bottom" in the tile (not sure what that means)
3:1338:9489:28416 3:1338:9489:12195 4:1308:18385:15890 4:2308:17861:17644 3:2630:7835:29684 3:1630:10818:30624
Does anyone have an idea of what may be going on?
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