Question: Mutations and copy number variations from DNA-Seq
gravatar for ciemanek
2.4 years ago by
The Netherlands/Amsterdam
ciemanek140 wrote:

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,


sequencing cnv snp dna-seq cna • 670 views
ADD COMMENTlink modified 2.4 years ago by Amitm1.9k • written 2.4 years ago by ciemanek140
gravatar for Amitm
2.4 years ago by
Amitm1.9k wrote:


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.

ADD COMMENTlink written 2.4 years ago by Amitm1.9k
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