I have already ran

sarek

on 20 WGS samples from patients with the same cancer and the pipeline took a while to complete due to them being sequenced to 90x coverage. 1. Can I run

oncoanalyser

on any of the outputs of the sarek run? 2. These samples are from FFPE tissues (tumour only). Can this pipeline filter variants (artifactual or otherwise)? 3. My initial aim is to find variants that are common between most samples.

Hi Cathal, thanks for your message. Your sample's coverage is typical for what we do internally. However, our tools have been designed for fresh frozen samples but you could try them out and see what you get. For the analysis starting points, you can check here but you can start from aligned or unaligned files. Hope this helps!

@Cathal many users have used it successfully on FFPE tumor only data but it is an area of development where we expect improvements to come. Since you're interested in common variants it should work well and run quickly on your set.

Thanks @Rayan Hassaïne and @Joep de Ligt Ill try the pipeline on my data this week!