Calling structural variants from RNA-Seq data

Question

[Yasin Uzun]

Hi,

I know that it is possible to call SNPs, indels using the GATK pipeline. However, I wonder whether it is possible to call large scale variants such as copy number variants (CNVs): deletions, duplications, translocations, etc. from RNA-Seq data and whether there is any pipeline or tool doing this. I will appreciate any comment about this issue.

[barslmn]

There are new studies about detecting structural variants from RNA-Seq. This blog about RNA-seq is a great resource: https://www.rna-seqblog.com/?s=CNV