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When creating a structure which has a variant type, and that this type is wrapped as an `Option`, the `unwrap` branch cannot be removed by LLVM, even after proving that the only path reachable is the …
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Almost in all instance where we use raw multihash we find ourselves capturing payload size an the side. It is also probably worth calling the fact that somewhat recently [fr32-sha2-256-trunc254-padded…
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**Describe the bug**
I'm working with SARS-CoV-2. I only want to incorporate indels into a variant call file with `ivar variants` and consensus genome generated with `ivar consensus` when a certain f…
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The desired behavior is the option to choose to run either or both of the preprocessing or variant calling parts of the pipeline.
Currently the implementation executes both parts as one pipeline.
T…
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Hello there!
I am interesting on using StrainFacts, but for various reasons using a metagenotyper like GT-Pro does not work well for my data. My plan is to profile SNPS using GATK, and extract the …
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Long TODO lists don't get done.
We are trying to keep an issue open if a real effort is happening to resolve it.
The below priority list gives a sense of where bcbio is heading in the next two rele…
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10:13:02: Executing task 'androidDependencies'...
Executing tasks: [androidDependencies]
> Configure project :app
WARNING: API 'variant.getAssemble()' is obsolete and …
Yi-Z0 updated
5 years ago
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The main challenge with using this pipeline for ATAC-seq data is the use of STAR for mapping within the WASP subworkflow. We could create two new mapping rules within the WASP subworkflow that use `bo…
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Hi Jeremiah,
I wonder if you provide example BAM files and output file (.vcf) that I can test svaba and replicate the result. It is because I like to test whether I am running svaba correctly or n…