Davide Bolognini

Hey @Overcraft90, the executable is in /opt/gfaestus/target/release/gfaestus. I can't run docker in the HPC we have, but for singularity (very similar to docker): ```bash singularity run gfaestus_v0.1.0.sif /opt/gfaestus/target/release/gfaestus --help ```

Hi @Overcraft90, sorry I did not give more details in advance. _And thanks. However, just for me to understand since I'm running this on a local workstation, can the former...

Hi @Overcraft90, the container now includes vulkan-tools and gfaestus can be run as follows: ```bash singularity pull docker://edg1983/gfaestus:v0.1.0 singularity run --nv gfaestus_v0.1.0.sif gfaestus ``` But still there are issues. @chfi,...

Hey @infotmatician, the example line you provide basically substitutes 1:10000-30000 with 20:420000-440000 (length here is 20000) and viceversa. That's what a reciprocal translocation is supposed to do. A simple script...

Hey @Jiayi-Wang-Joey, sorry for the delay, I'm travelling these days. I assume copy numbers here are deletions and tandem duplications. For tandem duplications, you have how many times a segment...

Hey @tomvanschaik, sure. I'll push a fix in the next days. Thanks, Davide

Hey @lx-1011, I would say that this is expected since short reads have limitations with large SVs and are splitted at breakpoints. Highlighting soft-clipped bases should help. Let me know...

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...

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).

Hi @agolicz, I know this has been a while but I'm trying to follow up on VISOR's issues and try to have them fixed by the end of the year....