Mutations and copy number variations from DNA-Seq
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3.8 years ago
ciemanek ▴ 140

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

SNP sequencing DNA-Seq CNV CNA • 951 views
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Entering edit mode
3.8 years ago
Amitm ★ 2.1k

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.

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