Somatic Structure Variation on exome-seq data - pipeline recommendations?

Question

[wiki97]

Hi, I am new to exome-seq and would be grateful for any suggestions :)

I am planning to use GATK4 to perform Structure Variation analysis on whole-exome seq data (somatic).

My question is - is there any GATK workflow available to perform such an analysis? Or maybe do you recommend any other pipelines for such an analysis on exome data?

I would be most grateful for any help :)

Answer 1

[Pierre Lindenbaum]

My question is - is there any GATK workflow available to perform such an analysis?

WDL: https://github.com/broadinstitute/gatk-sv

A structural variation discovery pipeline for Illumina short-read whole-genome sequencing (WGS) data.

[wiki97]

Dear Pierre Lindenbaum, thank you very much for your answer!

However I am still not sure because this pipeline is designed for whole-genome seq and I found that it will not work for exome sequencing data: https://github.com/broadinstitute/gatk-sv/issues/57

Someone recommended GATK CNV: https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-common-and-rare-germline-copy-number-variants

but this will give me only the copy number, not the information about the structure variation..

Do you know any pipeline for exome-seq data? Maybe not from GATK?

I would be grateful for any suggestions!