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There are a number of packages used by bcbio that depend on log4j, including fgbio, hmftools, gridss, picard, break-point-inspector, gatk, bcbio-variation.
Since these tools are not connected to we…
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Hi!
Thank you for maintaining this great workflow!
I've run into java problems after a fresh install of v1.2.9, see traceback below
```
Traceback (most recent call last):
File "/home/bcb…
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Hello,
I have {graph_name}.full.gbz files generated from Cactus Minigraph to map short-read data. According to the tutorial, a filtered graph is more efficient for vg giraffe. Additionally, I notic…
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**Is your feature request related to a problem? Please describe.**
Pathnames in Snakemake can get very long, and command lines even longer. This helps with data organization by explicitly encoding …
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Dear bcbio developers,
I am wondering if StringTie v2.2.0 with CRAM support is in the latest bcbio release of dev version?
CRAM support was only recently added to StringTie.
https://ccb.jhu.e…
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#### Kristie inquired regarding the adapter trimming from the vendor (who provides the sequencing library kit) and the following information was shared with us:
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Hello Kristine,
To trim…
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Bug occurs in the function to extract Read Groups from Bamfile. This is used in longread analysis before minimap2.
https://github.com/imgag/megSAP/blob/358d1de90507f173d1a4b262b3db4dcf0cf9625e/src…
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Thank you for developing this awsome tool.
I would like to know what is the best practice for selecting a unique transcript based on vep2maf. I am in a clinical analysis scenario, focusing on dozens…
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### Description of bug
I have a bunch of "test" samples to develop a bacterial WGS pipeline against. Part of that is running Kraken2 to profile the taxonomic composition of the reads.
I found that…
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### Feature Request ✨
It'd be nice to highlight our organization here on GitHub. An organizational level README would help with that. Additionally, we could use it as a place to coordinate all our …