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I installed snippy v 4.6.0 and snpEff version SnpEff 5.1d (build 2022-04-19 15:49). When the reference file is a .gb file, I encounter the following error
[19:30:07] This is snippy 4.6.0
[19:30:07] …
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I am running snippy using following command. However, it shows the following error..
snippy --cpus 8 --outdir variants --ref reference.gbk --R1 trimmed_S_010_R1.fastq.gz --R2 trimmed_S_010_R2.fastq…
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### Hi Strelka2 Team,
I am using the release `strelka-2.9.10`
After running strelka in a somatic way for whole genome, we tried to annotate the strelka's vcf with snpEff; That tool (snpEff) show…
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Hi,
thanks for this great work.
I tried to reproduce the results using the README instructions. However I got this error.
`NameError: name 'picard' is not defined`
Here what I have done (afte…
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Hello,
I have a MTB strain with a large deletion in pncA gene, that should leed to LoF. In a previous version of tb-profiler this deletion reported resistance to Pyrazinamide (as well as in the cu…
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When looking at the Local Data/Data Managers page of the Admin menu, data managers with more than one version installed are shown for each version in the left hand column. However, no version numbers …
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I'm getting an [error trying to feed `Varscan2.3.9` data into `SnpEff`](https://github.com/pcingola/SnpEff/issues/267#issuecomment-736928876). The developer says this is because the `ID` column is mis…
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"It compiles prediction scores from four new and popular algorithms (SIFT, Polyphen2, LRT, and MutationTaster)"
arq5x updated
10 years ago
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Hi @aysegokce ,
I'm currently trying to replicate your testing on COLO829 using the COLO829 nanopore data provided by epi2me labs.
The workflow likes: `Clair3 -> whatshap phasing and tagging -> s…
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as mentioned in the inputs:
4) SnpEff file (for Format Specifications, see Part 2)
5) gff file (for Format Specifications, see Part 5)
thanks