Diagnosing issues with sample output

[waemm]

Hi,

Thanks for creating a great tool, its been a pleasure to use thus far! I have been processing some tumor only data and I have a handful of samples that look terrible, they have short segments, very few intervals per segment and I get plots like the one below - (good sample on the left for comparison).

I am not sure what to make of this, was hoping you could give some insight into what could be going wrong here - my assumption the quality of the DNA must be compromised in some way. The coverage of this sample is great though 300x and general multiqc metrics look fine.

Some questions

1. Could this be a sample processing issue or linked to sequencing or sample processing?
2. IS there a way to recover this sample? Any parameters I can use to try extract something more sensible from the data?

thanks!