Overlapping/conflicting variants?

Question

Overlapping/conflicting variants?

flashton2003 opened this issue 4 years ago · 6 comments

flashton2003 commented 4 years ago

Hello,

I'm having trouble interpreting the reported variants for one of my samples. Three variants in pncA were reported:

pncA_T80TG-A2289162CA:76:470:3062, pncA_G81GG-C2289161CC:51:470:3167, pncA_G82GG-C2289160CC:56:470:3146

Could you help me in interpreting these?

Thanks,

Phil

Answer 1 · 2020-12-09T09:46:06.000Z

Hi Phil,

Those are all the same insertion of a G. In gene coords, they are T80TG, G81GG, G82GG. So the insertion is TGG -> TGGG, it's just that you can add that G in 3 "different" places.

This raises a question though. @iqbal-lab do you think next time we update the catalog we should remove duplicate representations of the same variant?

Martin

Answer 2 · 2020-12-09T10:59:02.000Z

Thanks Martin, that makes sense.

Answer 3 · 2020-12-09T12:58:02.000Z

ugh. yes. v sorry @flashton2003

Answer 4 · 2020-12-09T13:33:52.000Z

ok, leaving this open as a reminder to do this when we make the next panel.

Answer 5 · 2020-12-09T14:16:35.000Z

@iqbal-lab no problem Zam!

Answer 6 · 2022-09-12T06:18:00.000Z

This is actually the same issue as #148. Closing this in favour of #148