-
I don't really know exactly how to title this issue, but I posed the question in Slack and Ratul suggested making an issue to track.
## Use-case
The reason I am looking for this functionality is…
-
### Operating system
ubuntu 20.04
### Platform
64bit x86
### OpenSlide Python version
openslide.__version__
### OpenSlide version
4.0.0
### Slide format
svs
### Issue det…
-
The pairwise alignment done in `rescue_mate` cuts out a much larger segment of the reference compared to when we can use seeds. This makes the pairwise alignment much slower for those instances (anecd…
-
Hi,
I'm currently working on benchmarking VCF files generated from HG002_data(test_run just one sample) for SV calling(Manta, lumpy, GRIDSS, nf-core/sarek) against a truth set. I aligned the BAM file…
-
Hello,
I'm trying to use Graphtyper as it seems to be fast and to scale well to many samples. Very easy to install and run so far.. but I'm unsure that I'll be able to make the most of it.
My unde…
-
Hi all,
I would like to know if anyone has ideas on how should I get the SV types (INS/DEL/INV) from the output vcf of minigraph>cactus>vg-giraffe>vg-call pipeline. Are there any tools I can use? O…
-
the link to the blog post is broken do you have a new web page?
-
HI I'm sorry if this issue is recorded somewhere else; I couldn't find it although I imagine you're well aware of it. In summary the sd-app on the SecureDrop Workstation does not handle content that h…
hoyla updated
10 months ago
-
Hi,
I was playing around with the pyvips image loaders new_from_file and openslideload. I noticed that when you write an image using pyvips and then load it using openslideload, then openslideload …
-
Not an issue as such (apologies), but do you have any advice regarding possible merging of the sv.vcfs into a multi-sample file?
bcftools norm/merge fails due to the ALT and GT encoding being 'inc…