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Whole Genome sequencing, Copy number Variation

Hi I have whole genomics sequencing data from non tumor samples(by complete genomics). I am browsing through R packages to determine which will be best suited to analyse for copy number variants in the data. I also want to analyse for denova cnv's, for this purpose I have family data from healthy parents and children with neurodegenerative disorders.

Any inputs will be appreciated.

Thanks

whole-genome-sequencing cnv r complete-genomics
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updated by Ram Ram • written by Mani • Mani

2 answers

There are tens of programs that will do this in various ways and with varying speed and accuracy. Have a look through Zhao (2013) Bioinformatics for a relatively recent review of many of them.

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updated by Ram Ram • written by george.ry george.ry

Thank you George. In my case I already have called CNV data (based on read depth) and want solutions for efficiently analysing the data.

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updated by Ram Ram • written by Mani • Mani

Here another review that compares different computational methods suited for somatic copy number detection.

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updated by Ram Ram • written by Nicola Casiraghi Nicola Casiraghi

Thank you Nicola.

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written by Mani • Mani

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