Multiple overlapping homozygous calls

[ljohansson]

Dear @tjiangHIT,

I am analyzing ONT data and was wondering what is the cause for the calls belown. It seems like the same inversion is called three separate times.
Do you have an idea what could be the cause of this? Is this wat to expect, or is something goint wrong?

chr8    6297863 cuteSV.INV.464  G       <INV>   162.2   PASS    PRECISE;SVTYPE=INV;SVLEN=1907;END=6299770;RE=19;STRAND=++;AF=0.9048     GT:DR:DV:PL:GQ  1/1:2:19:162,35,0:34
chr8    6297864 cuteSV.INV.465  G       <INV>   86      PASS    PRECISE;SVTYPE=INV;SVLEN=1906;END=6299770;RE=11;STRAND=++;AF=0.8462     GT:DR:DV:PL:GQ  1/1:2:11:86,14,0:14
chr8    6297864 cuteSV.INV.466  G       <INV>   267.2   PASS    PRECISE;SVTYPE=INV;SVLEN=1906;END=6299770;RE=30;STRAND=--;AF=0.9375     GT:DR:DV:PL:GQ  1/1:2:30:267,63,0:62

Regards,
Lennart

[Meltpinkg]

Hello, @ljohansson

Under normal circumstances, this inversion should be reported as two entries with strand fields "++" and "--", which represents the strand form of the inversion. It respectively corresponds to one of the first two lines and the third line in your results. Clearly, the first two lines provided are reduplicated, which is likely due to an error.
If possible, could you please provide a subset BAM file around the inversion site (e.g. for the region around chr8:6297563–6299970)? This would greatly assist us in diagnosing and resolving the issue.

Thank you for reporting this issue to us, and we will continue to follow up on this issue.

Best regards,
Shuqi