CNV, CNA and SNP calling

Question

[Pin.Bioinf]

Hello,

I have a very basic question because I have never worked with SNPS or CNVs:

If I have many tumor samples and many normal samples from different patients, am I supposed to be calling the CNVS and SNPS for each patient? Like: tumor patient 1 vs normal patient 1

Or am I supposed to compare all at the same time like in a differential expression analysis?

Thank you

Answer 1

[Nicolas Rosewick]

You should compare the pair samples (tumor and control) from the same patient. Not all tum vs all control.

[Pin.Bioinf]

Thank you! And then, what is the statistics applied to draw a conclusion from all individual comparisons? (Im not there yet, but its curiosity)

[WouterDeCoster]

We don't know what your biological question is.

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

[Nicolas Rosewick]

As Wouter mentioned it depends on the related biological question.

[Pin.Bioinf]

Okay. What I actually want to observe is if there is a SNP and / or CNA change in a same tumor along time. So I am using tumor at time 1 as control and tumor at time 2 as tumor in Varscan . Is that correct? Because I want to see the changes in between. Or maybe i should call for snps and cnas individually for each tumor (like varscan allows to do) and then compare both .tsv files and see if there is a difference in there.?