search

davidebolo1993 / VISOR

VarIant SimulatOR for short, long and linked reads
GNU Lesser General Public License v3.0
41 stars 11 forks source link

Inquiry on genotype of SVs #26

Closed ngaitan55 closed 1 year ago

ngaitan55 commented 2 years ago

Hello! I am using VISOR to simulate SVs and reads following the pipeline specificated in the documentation page. I am using these simulations in order to perform a benchmark of an SV caller I am developing, thus, I need to also benchmark the genotyping accuracy against other tools. My question is if there is some way I can obtain the genotype information for the Gold Standard callset for each variant such that I can calculate the accuracy of any caller in terms of the genotyping assignment. Thank you very much!

davidebolo1993 commented 2 years ago

Hi @ngaitan55, sorry that I'm late on this but I didn't receive the related notification. In principle, your genotype is known because you either simulated hom/het alterations. Can you provide a more specific use-case ? What do you need to have for benchmarking ?

Thanks,

Davide

ngaitan55 commented 2 years ago

Hi! No problem. So i used the pipeline specified in the VISOR docs for random simulated SVs over a A.thaliana reference genome, but I did not see in any step what genotype did I simulate. I only generated one haplotype. So i would need to know the genotype of each SV, but then if you tell me all the SVs have the same genotype i would need to know how to learn what it is, thanks!

davidebolo1993 commented 2 years ago

If I got this right (one haplotype with SVs inserted) and you simulated with SHORtS/LASeR, then you have all HOM variants (all reads are from the modified haplotype).