Mutations and copy number variations from DNA-Seq

Question

[ciemanek]

Hi All,

I have a basic question about variants calling and copy number calling - I didn't have anything to do with the latter so far but I wonder if the experiment differs significantly? I have NGS data from which I was calling variants but I was thinking of utilizing those also to analyse Copy Number Variation, however I don't quite understand if I can use this data.

All the best,

Agata

Answer 1

[Amitm]

hi,

You can perform CNV analysis using NGS data, provided the depth of coverage is sufficient. I think ~60x mean depth is decent for whole-exome. This review is a good starting point for choice of tools.

A recent development is the use of off-target reads, along with on-target for better calls. This is one such tool.