tumor fraction estimation and fragment size plot using sWGS data

Question

[J.F.Jiang]

Hi all,

We have sequenced several cancer patients' ctDNA, and get some sWGS data.

In order to compare the data before and after treatments, we want to focus on the fragments and tumor fraction.

Besides ichorCNA, is there any other tool that can correctly estimate the tumor fraction?

And how to plot the fragment size profile as the figure listed below?

Thanks, Junfeng

Answer 1

[yussab]

Dear Junfeng,

I'm interested in your same subject. I'm trying an R library called cfDNAtools, it's able to determine fragment size and minimal residue, but it's not suited for tumor fraction calculation. Do you have any insight in which tool are you using?

Best regards,

Youssef