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Hi Fritz,
Thanks for the tool.
Is there an option for SURVIVOR not to change the SV type from BND to INV where both breakpoints are on the same chromosome?
Because some variant callers do not…
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Good afternoon,
I am using the following code to report variants for some targeted sequencing analysis samples.
After applying the following code, I could see how the low frequency variants wer…
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Reading in vcfs from variant callers that run on long-read bams is only part of the problem. MAVIS still needs bam files for most operations. Such bams have a few key differences from short-read ("NGS…
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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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I want to ask whether variant callers within MetaPpo can only use reads of a certain regions or chromosomes, so there is no need to filter the BAM file. I ask this because I have used extra reference…
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One thing that I've found underspecified when using `@overload` is what the type signature of the actual function should be.
For example, let's say I have a function like:
```python
from typing…
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Hey Brent,
I've been testing this out recently and I really love how fast it adds the annotations. I have a particular use case, and it may be something you don't want to support, but I thought I wou…
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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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Many of the peak callers mentioned in #2 have a ton of parameters. Some matter, some don't. Making note of which ones are worth making available to the user and which should just use default settings …
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**Is your feature request related to a problem? Please describe.**
Variant calling procedure infers genotype from positive and negative strand for paired end reads. The genotype can be different betw…