search

andersen-lab / Freyja

Depth-weighted De-Mixing
BSD 2-Clause "Simplified" License
100 stars 29 forks source link

Identical Abundance Result #154

Closed whottel closed 1 year ago

whottel commented 1 year ago

Hello,

On a few lower quality samples, I have noticed that the same abundance result is recorded across several lineage (please find attached example). S190_demix.txt

Any thoughts on what might be causing this?

Thanks, Wes

joshuailevy commented 1 year ago

Hey Wes,

Sorry for the delay. It looks like given the available sequencing coverage, Freyja is assigning equal likelihood to each of those XBB.1.5 lineages (which it represents by assigning equal fractions to each lineage). We are actually about to release some functionality that will automatically group lineages that are indistinguishable given the available genome coverage that will help out with this case (as well as some of the convergence errors that can happen as a result of these identifiability issues).

Josh

whottel commented 1 year ago

Hi Josh,

Thanks for the response, I will be on the lookout for the udpated version.

-Wes