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CNV - Copy number variations. Which tool is most used for?

Hello! Like in the title. Which tools is now for CNV most useful and have the most functions?

Thanks in advanced for reply.

number variations cnv copy
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updated by Kevin Blighe Kevin Blighe • written by ja4123 • ja4123

Are you working with southern blotting, microarray data, exome sequencing, genome sequencing, single-cell transcriptomics, ATAC-seq, or long-read sequencing?

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written by WouterDeCoster WouterDeCoster

Thanks for reply. Microarray data, single-cell transcriptomics and whole genome sequencing.

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written by ja4123 • ja4123

In that case, you will have to use different programs for each technology. For example:

  • Microarray data --> which array type and vendor? It is important to know
  • single-cell transcriptomics --> infercnv (R)
  • whole genome sequencing --> Battenberg (R), HMMcopy (R), and others
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written by Kevin Blighe Kevin Blighe

What you mean by "vendor"? It is possible to do analysis in python? There are some packages for that?

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written by ja4123 • ja4123

1 answer

Vendor: Illumina, Affymetrix, Agilent, or something else. It is important to know this due to the fact that Microarrays can be very different in how they probe genetic material.

Regarding Python, one could search the World Wide Web. My own quick search reveals these:

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written by Kevin Blighe Kevin Blighe

Thank you very much!

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written by ja4123 • ja4123

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