Where to find control samples for CNV calling tools.

Question

[mafonso]

Hi,

I am a newbie in Genome sequencing and I'm trying to run the available softwares to recognize CNV.

I have data from a lab (.bam files and .bed files). The issue is that the software that I have tried (CONTRA, EXCAVATOR, etc) require test and control samples (.bam files).

My idea is that the control samples are fine and don't have any variations. Is that it? How can I get those files?

Thanks you very much for your time.

Mariana

Answer 1

[Istvan Albert]

The point of control samples is that assuming that there is no detectable variation is typically unsound. Not having valid control samples will make the processes described in the paper invalid.

Read the Methods and Materials section for more details.

If you found other published data that from tissues and preparations that are very similar to your data you could perhaps use that as your control.