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Hey Guys,
I'm seeing the following error for a somatic_wgs run:
```
2022-11-20 11:58:36,779 cromwell-system-akka.dispatchers.engine-dispatcher-5918 INFO - WorkflowManagerActor Workflow e1ad4b2…
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Hi,
We use somaticseq to just merge variants from Mutect2 and HMF Tools SAGE (the latter as "arbitrary" vcf's), the classification module is not used currently. However we were missing some multi-n…
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### Board Type
RaspberryPi3, but not relevant.
### Operating System
Raspbian, but not relevant.
### Swift Version
Pre-built 5.1
### Description
Rather than call `abort()` when an …
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I noticed on the [Basic Operations][0] wiki page that there are two types of genotypers contained within `vg`: `vg call` and `vg genotype`. The documentation on the "Basic Operations" page notes that…
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Consider the following results from the micro benchmark at the bottom of this issue description:
Notice how the "on function" variants are significantly slower AOT than JIT.
If we remove the "in…
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We recently accessed several of the pcawg variant calls and realized that based on the name of the files, it was likely that the `delly filter` step was being omitted, since the naming pattern was `.e…
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### Subject of the issue
I need to fill in missing genotypes on a union .vcf of ~230 horses (depth of coverage: 2-60x) and 3 different software callers. Due to computational limitations I have had to…
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Hello,
@dlaehnemann mentioned adding varlociraptor to a benchmark we have set up in #157, and I have some questions about recommendations for setting that up.
We currently have an internal bench…
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I have enjoyed using Clair3 (clair3-arm64) for examining natural variants at the whole-genome level. However, I've recently noticed some irregularities that likely need correction.
Specifically, I …
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Hello Brent- This work looks very promising, I'm going to keep my eye on it's development for sure.
Also: I encourage you to investigate octopus!
We use octopus as the variant caller in our c…