This is a test version of Biostars. For the public version, visit https://www.biostars.org.
tumor fraction estimation and fragment size plot using sWGS data

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?

enter image description here

Thanks, Junfeng

ctdna ngs wgs
• 1,094 views • link
updated by Ram Ram • written by J.F.Jiang J.F.Jiang

1 answer

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

• 0 views • link
written by yussab • yussab

Log in to answer this question.

More posts like this