Hello, I am interested in using the nf-core/oncoanalyser pipeline for homologous recombination deficiency (HRD) analysis. I have a couple of questions regarding the compatibility and usage of the pipeline with specific data: 1. Compatibility with IonTorrent BAM Files: Is it possible to use nf-core/oncoanalyser to analyze BAM files generated by the IonTorrent platform? If so, are there any specific considerations or adjustments that need to be made when importing these files into the pipeline? 2. Using the Oncomine Comprehensive Assay Plus (Thermo Fisher): I would like to know if it's feasible to use nf-core/oncoanalyser for HRD analysis with data from the Oncomine Comprehensive Assay Plus panel by Thermo Fisher. Although the documentation mentions support for the TSO500 panel, I am curious whether a similar analysis can be performed with the Oncomine Comprehensive Assay Plus panel, and what modifications might be necessary. Thank you for your assistance and for the excellent work on this pipeline. Best regards,

Hi Nour-eddine, thanks for your message! How big is your panel? In our experience, TSO500 is around the bottom limit of the panel size to cover sufficient regions to reliably detect HRD (for a tool that is trained on WG)

Hi @Rayan Hassaïne, Thank you for your feedback. The Oncomine Comprehensive Assay Plus panel I’m using targets around 500 genes, covering key regions for oncology. Do you think this would be sufficient for reliable HRD analysis, even though the pipeline is optimized for larger coverage panels like the TSO500? Are there any specific adaptations or adjustments you would recommend to improve the reliability of the results with this panel?

Hi @Nour-eddine Sadiki, oncoanalyser currently does not offer HRD analysis for targeted sequence data. However, I’m aware there is some discussion around improving support for this in the future

Hi @Stephen Watts Thank you for the quick response and for connecting me with the hmftools developers. Could you please provide me with the best way to get in touch with them? I'm particularly interested in discussing HRD analysis with Ion Torrent data and how it might be approached using the Oncomine Comprehensive Assay Plus (OCAP) panel. Thanks again for your help, and I look forward to any updates on future developments in this area. Best regards,

Hi @Nour-eddine Sadiki I’ve cc’ed you in on email (the one in your profile) with Peter and Charles

Hi @Stephen Watts Thank you for the email. I have received the email you cc'ed me on : ).

No worries!