Genotyping CNVs from Next Generation Sequencing data

Question

[QVINTVS_FABIVS_MAXIMVS]

I am developing a method to genotype CNVs from next generation sequencing data.

Aside from SVtyper, do people know of other algorithms that can perform the same function?

I'm looking to compare my method to others.

Edit: Preferably NOT specialized for tumor samples.

Thanks!

Answer 1

[Zev.Kronenberg]

Below is the short list of tools that I know of for estimating copy number state and genotype. From personal experience, this is a really crowed field and completive.

Genome strip, CNVkit, Wham, Delly, CNVnator, WSSD.

[QVINTVS_FABIVS_MAXIMVS]

That's true but what about copy number estimators that use machine learning on positive examples?

[Zev.Kronenberg]

If regression trees are good enough: http://www.nature.com/nmeth/journal/v12/n6/full/nmeth.3394.html#ref23

I'm not sure what you mean by positive examples? Medically relevant biological true positives?