Updated analysis: Fusion filtering (annoFuse) bug

[jharenza]

What analysis module should be updated and why?

For NTRK1, and unknown how many other genes, the get_Pfam_domain.R function is showing two kinase domains when there should only be one annotated. This is causing a mis-calculation in whether or not the domain is retained, specifically for BS_KP735TJ6 (PT_MSQ6GSVP) in the IHG subtyping PR for HGGs

What changes need to be made? Please provide enough detail for another participant to make the update.

Unknown - need to investigate - is this using more than one transcript even though we thought we were only using canonical?

@zzgeng is going to look into this some more

What input data should be used? Which data were used in the version being updated?

When do you expect the revised analysis will be completed?

Who will complete the updated analysis?

[jharenza]

UPDATE: there are 42 kinases which have more than 1 kinase domain annotated: https://github.com/d3b-center/annoFuseData/blob/update-pfam/pfam_update.R

@zzgeng will work on identifying (manually, cringe) the domains which should be removed if these genes only have 1 (which likely is the case!!)

[jharenza]

PR: d3b-center/annoFuseData#8

[jharenza]

completed in d3b-center/OpenPedCan-analysis#316, d3b-center/annoFuse#99