Using oncoanalyser for whole exome sequencing data

[anshupas]

I have whole exome sequencing data from tumor and their matched normal samples. Can I use oncoanalyser to process this data e.g. by setting the mode to wgts?

[p-priestley]

We would recommend that you run oncoanalyser in targeted mode using resources trained for your specific exome panel (which may differ across vendors). An overview is described here:

https://github.com/hartwigmedical/hmftools/blob/master/pipeline/README_TARGETED.md

Which exome kit are you using? We may be able to help provide some pre-trained resouces. If you are interested please email me at [email protected]

[anshupas]

Thanks for clarifying. We are interested in using oncoanalyser for whole exome sequencing data, I have emailed you the relevant details regarding this.

[scwatts]

Closing this issue as resolved, thanks for fielding @p-priestley