Dear Sheila, and Geraldine,
congrats to the team that is developing MUTECT2 ! it picked a LINE1 insertion in TP53 that was not picked by any other caller ....very impressive !
Thanks @Bogdan, we'll let the team know -- I'm sure they'll be very pleased!
As expected the team is very pleased! They ask if it would be possible for you to share a snippet of the bam file for them to use as a test case. This would help protect against regressions, i.e. ensure that future versions continue to detect this type of variant (which sounds like a difficult case, if others are all missing it). Of course we understand it may not be possible if it's protected patient data, but it doesn't hurt to ask
HI Geraldine, thanks, I have your email address, and I could email you soon. thanks !
Actually, we have a secure way to transfer files that won't go to our email. Have a look at this article.
certainly, we can do it in that way ! thanks !
Just uploaded the files, the folder is named "LINE-1-insertion-in-TP53". Shall any comments or questions arise, please feel free to contact me at [email protected]
Thanks. I will put this in soon.
This is indeed a cool case. Thanks for sharing
I put in the report.