Structural variation germline vs somatic ?

Question

[Picasa]

Hello,

I have tried multiple tools to call structural variants like Manta, Delly etc. They all have a germline or somatic mode.

I couldn't find this information anywhere but anybody know how these structural variant callers determine how a variant is a germline or somatic one ? What are the criteria ?

Thanks for your answers.

[Nicolas Rosewick]

do you have paired normal-tumor samples ?

[Picasa]

I am working with a non model species and don't have a normal-tumor samples.

But rather 2 haplotypes, and I am expecting one haplotype (let's call it hap B) to have a specifc inversion. Do you think I can "transpose" it like a normal-tumor samples so that would be hap A for normal and hap B for tumor ?

Answer 1

[metinyazar88]

This is a very controversial topic but you can read this article => https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4502642/ Especially last figure of the article can hep you.

[Picasa]

Thanks for your paper. Very interesting.