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

Question

[ja4123]

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

Thanks in advanced for reply.

[WouterDeCoster]

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

[ja4123]

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

[Kevin Blighe]

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

[ja4123]

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

Answer 1

[Kevin Blighe]

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:

• https://cnvkit.readthedocs.io/en/stable/
• https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-S11-S1/tables/3

[ja4123]

Thank you very much!

[Kevin Blighe]

You are welcome.