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I tested 2.17 to 2.24 using an inversion between two large homologous domains.
2.17 and 2.18 detection was possible using structural variant callers.
Everything after that was unable to be found.
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What's the deal with that?
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We assume in a couple of places that anything stored in the av-store has been checked for validity already, yet the av-store does not guarantee this invariant. Callers ensure that by themselves, e.g. …
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Hello,
I'd like to ask if there is a way of only keeping one INFO field when merging VCFs, meaning if there is a variant that is found by 2 different callers, only keep the INFO field of the 1st ca…
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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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Hi there,
This is more of an inquiry than an issue.
I just cam across your paper describing TIDDIT and wanted to give your software a test. I am wondering how to deal with ploidy. Though the or…
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This is a little bit of a classic! Since it will not be obvious between runs what callers were combined for `set=Intersection` merges (found by all callers). The `FOUND_IN` tag used by some other tool…
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This one is not an issue but more of a question, i was running multiple variant callers on the same bam and i realized that some variants are assigned a low quality in deepvariant (20 variants as i do…
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### Description
`serve.get_app_handle()` and `serve.get_deployment_handle()` and their underlying method `ServeControllerClient.get_handle()` allow users to dynamically get a handle to a Serve Depl…
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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…