-
Hi,
I am working on a structural variant breakpoint cluster classifier for cancer samples and was wondering whether you had a BEDPE format parser in the offing or whether you planned to write one i…
-
We should make a cancer genome demo
This would maybe involve
- Nice display of structural variants
- CNV display
- Maybe the linked-supplementary reads display, I think this is very powerful…
-
Palette swapping is hugely expensive (relatively speaking) in SDL2. This is especially noticeable with text due to the palette being swapped many many times per frame.
Specifically, I'm talking abo…
-
Hi there,
I am trying to run palimpsest https://github.com/FunGeST/Palimpsest.
Their SV requirement is
```
Sample: Sample identifier. Any alphanumeric string.
Type: Type of structural variant…
-
| structural_variant columns | mapped columns | remaining columns |
| ----------- | ----------- | ----------- |
| GENETIC_PROFILE_ID | mutation…
-
Hi,
My sample is WGS (cancer tissue paired with normal tissue). Ref is hg38. GRIDSS version is v2.9.4 docker. GRIPSS.jar version is v1.8/1.9 (both tried).
To get somatic event file, I used gripss…
-
Hi @d-cameron.
Thanks for your software. I got now a vcf file but it's difficult to interpret when you have only breakpoints.
I have used the `StructuralVariantAnnotation` package and the code…
-
If you are a current or prospective Landscape contributor, feel free to attend our weekly meetings to discuss the ongoing work on Landscape.
- Every Monday, 6:30pm to 7:30pm Eastern Time (Toronto /…
-
Hi there,
i am trying to use SVXplorer in order to call SVs in plant genomes. I have a few Issues regarding that. First, when I try to call on my full data set (around 60x coverage) I end up using …
-
Most structural variant callers output results in VCF. To simplify the output of one program as the input to another, it would be desirable to specify a VCF using `-d`.