Coordinates of CNV position

[reshu23]

Dear Team,
Thank you for developing awesome tool. I have one question regarding reported CNVs by Spectre. I was checking some reported CNVs in my dataset in the DGV database. I can see, coordinates are not exact coordinates(breakpoints) of reported CNVs in DGV database. But range is perfect. Should I assume that, Spectre wont report exact breakpoint?

Thank you.

[philippesanio]

Hi @reshu23

My apologies for the late reply.

Should I assume that, Spectre wont report exact breakpoint?

Yes, Spectre will not report the exact breakpoint. The reported start and stop position of a CNV is related to Mosdepth bin-size used for the coverage. E.g. when using Mosdepth with a bin-size of 1kb, the coverage positions available to Spectre will be in 1kb steps. Hence, Spectre can only report start/end positions in 1kb steps in this case. Which should be fine since, we are currently targeting large CNVs >=100kb.

If you have more question, feel free to ping me or post another issue any time.
Best,
Philippe

[reshu23]

Thank you.