Hey all, first of all thanks for the great tool and extensive documentation. I've seen some similar questions come by here already, but I still can't seem to figure it out. I want to run the oncoanalyser for my paired WES data. I got almost all resources file ready, however I cant seem to figure out how to build or find the

target_region_msi_indels

file. I couldn't find one for my panel, so I was thinking of maybe using my bed file to subset the msi file from the WGS pipeline but correct me if I am wrong, it does not seem to be included in the

hmf_pipeline_resources.38_v2.3.0--2

. Thnaks in advance for the help!

@Stephen Watts one for you?

Hi @Steven Wijnen, yes that’s right, you’ll need to manually construct the MSI INDELs file specifically for your WES panel if you want to run a MSI estimate. If you don’t want to run this estimate, the file can be provide with just a header and no entries

Thanks for the additional info! I think I will just leave it empty. Can't seem to find an appropriate file for the panel we used. Are the locations of the TSO500 based on the panel or the reference genome used? If it is the latter I could at least use the tso500 file to see what comes out. These regions mentioned are all sequenced in my panel.

The MSI sites file posted above is specific to the TSO500 panel, and the quality of the MSI estimate will depend on the panel and the defined sites