What does running SAVANA with ONT_noisy imply?

cortes-ciriano-lab / savana

Somatic structural variant caller for long-read data

Apache License 2.0

43 stars 2 forks source link

What does running SAVANA with ONT_noisy imply? #28

Closed MartinezRuiz-Carlos closed 4 weeks ago

MartinezRuiz-Carlos commented 1 year ago

Hi team,

I am working with SAVANA and ONT data and so far so good, I just had a question about the ont_noisy flag. Apologies if I have missed this, but I could not find information about when it might be preferable to use this flag as opposed to just ont? Is this dependent on the quality of the sequencing or other factors like, say, coverage or cancer cell fraction of the sample?

Many thanks!

helrick commented 4 weeks ago

Hi there,

Many apologies for my delayed response on this! In the latest release of SAVANA (1.2.0) we no longer use this flag. Previously, we distinguished our available data into "noisier"/R9 ONT flow cells and "less noisy"/R10 ONT flow cells and trained these models separately. However, to simplify things we now provide a unified model trained on all of our available ONT data. I hope this answers your question and also simplifies the execution of SAVANA.

All the best, Hillary