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9.1 years ago
Guannan
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Hello
Recently, I have been working on the comparison of plant genomes. And I want to identify SVs and CNVs in my samples. I have been looking for programs capable of doing this, but it seems the majority of the programs detecting CNV are designed for human, and compatible with other animal genomes or bacterial genomes, like CNVnator,Control-FREEC, cn.MOPS,PennCNV,etc. When I looked for papers citing these programs, they are all about human, animal,or bacterial genomes. Does anyone have the experience with CNV detection of plant genome, any suggestions or recommendations?
Thanks in advance.
Guannan
Hello, I am also looking for good CNV detection programs for polyploid plant genomes. Do you mind sharing which programs you end up using and how do you think about them? Thanks a lot!!
There a few CNV-related R packages available on the Bioconductor website. After reading the vignettes for the CNV and CNVtools packages it seems these can handle any genome, or for which an SNP array was used.