A software tool for gene copy number and loss detection

Question

[liorglic]

Hi there,
I was wondering if someone could recommend a software tool that can detect gene copy number variation (CNV) and gene loss (presence/absence variation - PAV) within a population, based on WGS data.
Sudmant, Peter H., et al suggests a method that makes sense, based on normalized sequencing depth, but I didn't see any published implementation. SGSGeneLoss is a basic option, but it implements a very simplistic model for gene loss detection.
Anyone has a better idea?
Thanks!

[Pierre Lindenbaum]

https://github.com/dzyim/List-of-Structural-Variation-Detection-Software

Answer 1

[Philipp Bayer]

I've made good experiences with cn.MOPS: https://bioconductor.org/packages/release/bioc/html/cn.mops.html (which overlap quite a bit with a simplistic SGSGeneloss approach based on mosdepth and some scripting :) )

Hecaton is new and looking at the paper, it's quite exciting, but it's tailored at plants and I'm not sure which species you work in: https://www.biorxiv.org/content/10.1101/720805v1

If you're working in humans, this review/benchmark is very comprehensive (but misses CNVKit) https://www.sciencedirect.com/science/article/pii/S0002929717304962?via%3Dihub

[liorglic]

Thanks! I work in plants so I should definitely take a look at this new tool.

Answer 2

[Costadia]

CNVkit allowed to detect CNV using pooled reference/matched sample/no reference.