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Got this error:
```
Error in checkAtAssignment("CNOlist", "stimuli", "numeric") : assignment of an object of class “numeric” is not valid for @‘stimuli’ in an object of class “CNOlist”; is(value,…
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Hi,
Does structural variant calling suggested [here](https://huishenlab.github.io/biscuit/docs/structural_variants.html) also work for targeted methylseq data?
Also, do you know of any tool/pipe…
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**Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.6.1/docs/FAQ.md**:
**Describe the issue:**
I am trying to add the flags --parse_sam_aux_fields=true --use_original_quality…
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To improve variant calling workflows, having a look at FP or FN called variants can be helpful. At the moment, these variants are reported in tables that are stratified. Having a step to unifiy these …
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Copying @vsatheesh's message from slack and https://github.com/isugifNF/GATK-flow/pull/16#issuecomment-2231427609 to a separate Issue, since this is unrelated to the SNPeff PR.
> After adding thes…
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1. Go to demo data,
2. Go to MYLK2,
3. View ClinVar variants (not counts),
4. Call on selected gene
Called variants never load. If you view counts, or remove clinvar view and then call again, called …
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along the process of updating the workflows for (3) different technologies, I had to remember porting over changes across the workflows targeted towards the tech.
But many of the "modules" are simila…
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Hi guys,
I follow the tutorial command in the wiki page [here](https://github.com/vgteam/toil-vg/wiki/Genotyping-Structural-Variants) for structral variants.
when comes to the `toil-vg call`,…
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Basically 3 parts, each part should have its own shell script file:
1. Retrieving SRA files (.fastq format) using EDirect and SRA-toolkit.
2. Quality control - trimmomatic and fastqc
3. Assembly and v…
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Hi,
I was using nanopolish variant v0.14.0 to call variant for consensus calling. I notice there are some positions in my virus genome that Nanopolish never registers that there is a variant despit…