How to compare two tumor samples?

[Jane M]

Hello,

I've worked on the comparison of a normal sample and a tumor sample in cancer data. I wanted to perform a direct comparison to detect somatic mutations, so I used VarScan2.
Now, I would like to compare 2 tumor samples, one untreated and one treated, in order to study the impact of a treatment.

I don't know if I can use VarScan2 here again, for a direct comparison. Maybe, the model is not suitable. I'm thinking about performing an independent analysis on both samples, but I would prefer a simultaneous comparison... I would like to ask you how do you do?
Thank you for your feedback,
Jane

[Jane M]

Any idea?

[honey]

Tumor samples

I would think same approach as you sued for normal vs tumor now you are comparing condition

[Jane M]

You mean, using varscan2 with untreated tumor sample as "normal" and treated tumor sample as "tumor"?
I don't know enough the model in VarScan to be sure that for the "normal", there is no assumption that prevents the use of tumor instead...
I don't know if I'm clear, do you see what I mean?

[arkal]

You mean, using varscan2 with untreated tumor sample as "normal" and treated tumor sample as "tumor"?
I don't know enough the model in VarScan to be sure that for the "normal", there is no assumption that prevents the use of tumor instead...
I don't know if I'm clear, do you see what I mean?

I don't think there should be much of a problem using the untreated as the "normal".... after all, all you want to do is test one against the other! Consequently, if you're still too apprehensive about doing that, you can use the untreated one as a reference and use publically available variant callers to call variants in your treated sample against your reference. check the first "sticky" post on this forum for a bunch of tools.