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### Actual Behavior
I install ensembl-vep from bioconda but the version is not the indicated 102.0, but 89.9
### Expected Behavior
the syntax has changed a lot from the old to the new…
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It makes sense to implement the extensive functionality offered by `IVar` to get from aligned BAM to consensus sequence. `Varscan 2` and `BCFTools` can still be used for metagenomics data too. We are …
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I'm running into an issue that I can't seem to solve. I think it has to do with multi-threading? Hopefully, you might have some insight into this.
Here is the error:
`set_mergeVcf.sh: Output file …
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After installing with pip3 and testing with the current repo, I tried swapping the columns (ours is tumor then normal) of a Varscan output file, and received the following:
```
$ neoepiscope swap …
jfass updated
4 years ago
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I'm trying to reproduce a pipeline previously written in our lab and there seems to be a discrepancy in the output which I've traced back to a `bwa-mem`/`bwa-mem2` difference (I think I've ruled out `…
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This issue continues from the previous one. Please see https://github.com/bcbio/bcbio-nextgen/issues/3194.
bcbio: 1.2.0
os: Ubuntu 18.04.4 LTS (Bionic Beaver)
yaml & logs: [bcbio.zip](https://git…
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@whoiswillma Hi, William. I maintain this third-party tap Brewsci/bio. I hear that you may have a script to automatically add licenses when it can be determined from GitHub or the source tarball. Woul…
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1. bamgineer/demo_codes/wes_example.sh is a blank file
2. I was also wondering if there are any demo files to try out bamgineer with? The directory bamgineer/tcga_experiments/inputs/ only contai…
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Hi,
I am afraid I am having another issue. An error at or after the formatting step. What do you think ?
My command line is
myresults = smurf(directory="Sample_test", mode="combined", check.pa…
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Hi,
I'm newbie at bioinformatic and I have one question.Do you recommend me some tool that is suitable to convert mpileup files that MTBseq generates to vcf files to visualize in IGV?? Or is it poss…