which software is the best to look at clinic structural variation in whole genome sequencing?

Question

[Ishak]

Dear Biostars

I would like to look at the best software I can use with Ubuntu to look at the structural variation in whole genome sequencing?

Any suggestion with thanks.

[ATpoint]

I hear that people like Lumpy https://github.com/arq5x/lumpy-sv

[cmdcolin]

when you say "look at" do you mean visualization or analysis

[Ishak]

Thanks for your question, I mean analysis

Answer 1

[d-cameron]

This very much depends on what sort of sequencing you did (short read, long read, fresh frozen or FFPE samples, depth of sequencing, and so on).

For germline analysis, two benchmarking papers came out around the same time showing broadly similar results:

https://www.nature.com/articles/s41467-019-11146-4

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1720-5

For somatic variant calling, I'd recommend GRIDSS2 (and PURPLE/LINX for downstream analysis) (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02423-x)