From FALCON to Canopy with multiple samples

[Simon]

Dear authors,

Thank you for the detailed material available on the repositories! I would be very interested to apply Canopy and, in particular, I have two questions:

1. Is there an automatic procedure or code available to get the allele-specific copy numbers from multiple WGS samples with Falcon and get the proper input Wm and WM for Canopy? Unfortunately the Falcon demo available on the Canopy repository (https://github.com/yuchaojiang/Canopy/blob/master/instruction/falcon_demo.R) and the Falcon instructions available on the section 4.3.2 of the MARATHON repository (here: https://rawgit.com/yuchaojiang/MARATHON/master/notebook/MARATHON.html#running-falcon-for-allele-specific-copy-number-profiling) refer to a single sample. As such, once I applied Falcon on each sample separately (is this right? as done in Falcon-x) how do I merge the samples and obtain Wm and WM from these outputs? Is there the need for manual inspection?

2. Can I run Canopy only providing the allele specific copy numbers Wm and WM?

Thank you very much for your help and support,

Best regards

Simon

[Simon]

Dear authors,

Just a quick update on question 2): I tried to call canopy.sample by providing R=NULL, X=NULL, and Y=NULL but all these inputs are required to be a matrix and the command failed.

Could you please specify what is the correct way to analyze only copy numbers WM and Wm without providing any mutation?

Thank you again for your support,

Best regards

[Yuchao Jiang]

Hi Simon,

Thanks for your interest in Canopy.

For your first question, there’s no currently no automatic pipeline to generate copy number input from FALCON to Canopy. The reason is because 1) there are a lot of false positives since the data is fairly noisy and from our experience curation of copy number calls after FALCON is really data specific and 2) you want to only focus on the regions where the samples show distinct copy numbers to relieve the computation burden. This is non-trivial yet it’s also not the focus of Canopy.

For your second question, the short answer is no. You can try Sequenza or ABSOLUTE but without somatic mutations the clonal structures can be very ambiguous.

Hope this helps!

Yuchao

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