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### Description of the bug
When I use my custom reference, error always show: This path is not available within annotation-cache. Please check https://annotation-cache.github.io/ to create a request …
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### Description of the bug
Hello,
I am running the "standard" pipeline with many variant callers, but suddenly got an error with Mutect2. The same command has worked previously for me for before. …
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Hi again, and thanks again for all the help with the great pipeline!
Now this error:
> ERROR ~ Error executing process > 'HADGE:run_multi:gene_demultiplexing:variant_freebayes:freebayes (sid456)'…
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[snps.log](https://github.com/tseemann/snippy/files/14536244/snps.log)
I met a problem when run snippy. I think it may relate to freebayes, but I don't know how to fix.
ps:snippy --check show "De…
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Dear author,
Thanks so much for developing the great tool. I recently applied it on a single nuclei data, and encountered some errors I have never met with 10x single cell data, here is the error:
…
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### Description of the bug
Hi am working with the pipeline, in the test working fine. with samples do not report the VARIANT_CALLING, there is no error in the run.
How I can make that processes?
##…
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my command:
```snippy --outdir test/mysnps --ref test/REF_GCF_904425475.1_MG1655_genomic\(1\).fna --ctgs test/11657_5\#1.fa"```
### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 -F 0.05 --m…
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The manuscript mentions, "Base quality is optionally determined using FreeBayes [54] to measure read support and mixed alleles."
I don't see that option in the v1.2 command line options. Also, I c…
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**In step2: Doesn't this command need to output a vcf file?**
freebayes -f -iXu -C 2 -q 20 -n 3 -E 1 -m 30 --min-coverage 6 --max-coverage 100000 minitagged_sorted.bam
**In step3: How is the in …
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I got this error like this. Does anyone can help to fix??
I run command on HPC:
snippy --R1 $p_trim/VN0467_1_paired.fastq.gz --R2 $p_trim/VN0467_2_paired.fastq.gz --outdir /lustre7/home/buihoangphu…