tool for the new protocol of WES for CNV detection

Question

[Sara]

to identify CNVs using WES data, I am trying to use WES data from a new protocol of Agilent Whole Exon V7 + CNV backbone which has additional regions added to the panel which is supposed to enable CNV for many known CNV regions. for this analysis I have used GATK for the old protocols but since this protocol has additional regions, what would be the best tool for CNV detection?

Answer 1

[Kevin Blighe]

There are countless CNV detection programs out there, but two that I, personally, hold in high regard are Control FREEC and HMMcopy.

Kevin

Answer 2

[German.M.Demidov]

I mean...you can even switch on off-target reads (~50KB should be fine) and run ClinCNV.... but well it is better to be used with >20 samples available...(can run for >10, but stat models feel better when there are >20)

(not necessary to switch on off-targets since you have backbone - but why not, these reads are for free)