Question: Structural variation germline vs somatic ?
2
gravatar for Picasa
8 weeks ago by
Picasa530
Picasa530 wrote:

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.

ADD COMMENTlink modified 8 weeks ago by metinyazar8810 • written 8 weeks ago by Picasa530

do you have paired normal-tumor samples ?

ADD REPLYlink written 7 weeks ago by Nicolas Rosewick8.8k

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 ?

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by Picasa530
1
gravatar for metinyazar88
8 weeks ago by
metinyazar8810
metinyazar8810 wrote:

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.

ADD COMMENTlink written 8 weeks ago by metinyazar8810

Thanks for your paper. Very interesting.

ADD REPLYlink written 7 weeks ago by Picasa530
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