CNA clonality for non-WES/WGS data

Question

[Jokhe]

Does anyone know any tools to detect copynumber variations (CNA) from matched tumor-normal sequencing data. There are tools like Battenberg and TitanCNA but they are intended to be used with WGS/WES data. My data, in turn, is a targeted sequencing data of 40 cancer genes. At least for Titan CNA my dataset is too small to be used.

Do you have any recommendations or tricks how to use my data for Batternberg/TitanCNA. From these option, TitanCNA would be more pleasing for me. As my project is related to tumor evolution, it is necessary to get information from CNA clonality.

Thank you in advance!

Answer 1

[ivivek_ngs]

Yes you can but with other tools if you are not restricted to explore new tools. Take a look at the thread.

Tools like XHMM, copycat2 and CoNVaDING can perform the trick of extracting CNV informations from your panel sequencing data.

Only thing is some of them have targetted panel of over 100 genes but I have not tried them. You can take a look and write to the developers in case you face issues.

[Jokhe]

Thank you! I tried to look previous threads but didn't notice that one!