adding samples for germline filtering

[Alessandro Bruselles]

Hi Tobias,

thank you for your work.

I have a pool of WGS (let's say 100), and I've called SVs following all the steps: 

- Called SV sites for each sample

- Merged all sites

- Genotyped the merged site across all samples
- Merged all genotyped samples

- Applied germline filter

Now, what if I have new samples that I want to analyse? After adding the new SVs to the already merged sites, do I have to re-genotype each time all the samples on the new sites before applying the germline filter, or there is another way to speed up the analysis?

Thank you

[Tobias Rausch]

Hi,

Yes, for the new SV sites you need to genotype all new SVs in all previous samples.

Best, Tobias

--
You received this message because you are subscribed to the Google Groups "delly-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to delly-users...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/delly-users/532de766-fda4-47a8-b86c-3f749bb9ff5cn%40googlegroups.com.

[Alessandro Bruselles]

Ok, thanks.