We have 15 control sample and 30 test sample and want to check copy number variation in test samples. The sequencing method used is ion-torrent PGM,
A region in a chromosome is targeted and the whole region is sequenced including intron and intergenic region.
Which tool is best to identify CNV in the samples?
Control-FREEC is one of the methods we found useful but the control sample are not matched normal, can we use multiple control in FREEC?