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In CPANG19, many students wanted to project a complex graph (not even alignments to it, but the paths in it) out to a VCF file.
It seems like `vg call` could be able to do something like this, shou…
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I ran into this when doing some testing and I haven't been able to figure out what the issue is so I figured I'd post. These are cows. Below is the beginning of the log for `phase_common` which runs f…
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Hi Erik,
I am doing some precision/recall analysis on a simulated set of 13 samples where each "sample" is a random mutant of a real-life plant chromosome. I introduced exactly 200 SVs per sample an…
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When hovering over the variant graph with the mouse pointer, a window opens up. Unfortunately, the data presented is very confusing:
1. It shows variants with zero frequency
2. The order of variants…
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Hi,
I am using `pandora compare` to call out the variants after building the pan-genome reference graphs and indexing them using `pandora index`. Although I am using multiple threads, it works with…
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It has been on my mind for a couple of years that the existing Parser and Serializer interface is a mess.
The current standard Parser interface predates multigraph support (from before `Dataset` an…
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Random order, sorry
- [x] ", which makes variant calling easier." -> add. Bacteria and yeast are typically also haploid. The same is true for most of the genome for highly-inbred strains of labora…
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**1. What were you trying to do?**
I have created some graphs from either PGGB or a multi-sequence alignment from 10 salmonella sequences, with a large (~1Mbp) inversion in the middle. Then, I wanted…
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I'm trying to layout what the restrictions on graph imposed by jVCF are. I'll list criteria and what may happen if they are not met
Possibilities:
* Graph is directed
If graph is not directed, …
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## Description
Eigen's QR decomposition can be improved on with better parameter tunning. GPUs can be used for further speedup.
## Example
QR decomposition is faster.
## Expected Output
QR de…
t4c1 updated
5 months ago