CNV detection for Ion PGM data

[tushardave]

Hello Folks,

I am newbie in CNV detection world. I would like to detect CNVs from Ion PGM data. I am aware that Ion PGM system data can be analyzed with Ion Reporter software for CNV. But I would like to develop my own pipeline. I would like to have some thoughts from you expert people for the development of my pipeline.

Thanks for your help.

Regards,
Tushar

[IonTom]

One of the problems with PGM data and CNVs is that you only analyse amplicons, so coverage over a larger region is not available. Sometimes you also have no access to nomal tissue. One solution i'm currently testing is the Biocondcutor package cnMOPS. This makes use of the coverage distribution over multiple samples and also works for smaller regions.

Needs some adapting and testing, but for this use case it seems like the best solution.

[tushardave]

Thanks IonTom.

Can you please briefly explain me the steps that I have to take to develop my pipeline?

Currently, I have BAM files from PGM.

Thanks for your help.

Best,
Tushar