Custom annotations in "Format" column

Skip to first unread message

Anselm Hoppmann

Feb 22, 2018, 9:26:25 AM2/22/18
to gemini-variation

Great work, thanks a lot.

I use gemini on a daily basis in order to filter for causal variants. I've also added some custom annotations like HGMD, but now I struggle with one annotation I'd like to add.

In order to get rid of variant calling artifacts I'm performing a consensus variants call with different caller and annotate the number of caller calling this variant in the "Format" column. It is important to keep it in the "Format" column since subsequently I merge data from different patients to load them together in one gemini DB, and individual patients can have varying caller finding variants. Unfortunately gemini doesn't integrate these informations in the database. Checking through the "annotate" option it seems to annotate per variant and not per variant and individual.

Thus my question, is there any possibility to add custom annotations in a patient based manner instead of variant based?

Thanks in advance,

Anselm Hoppmann

Brent Pedersen

Feb 22, 2018, 9:35:15 AM2/22/18
to Anselm Hoppmann, gemini-variation
That's not possible at this time. We only load depth, GQ, and genotype
stuff from the sample fields. If you inject your sample information
into those fields before loading then gemini should accept and use it,
but I'm guessing that doesn't address your use-case.

Anselm Hoppmann

Feb 22, 2018, 9:43:28 AM2/22/18
to gemini-variation

Thanks for the quick response. Unfortunately this work around doesn't help...

Would it be possible to add something like this for a future version? Loading all sample information would, in my opinion, increase the flexibility of the tool tremendously.


Reply all
Reply to author
0 new messages