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At the moment we use pre-calculated values for SpliceAI, that only look at "all possible substitutions (snv), 1 base insertions
and 1-4 base deletions (indel) within genes"
We had a potential splice …
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### Subject of the issue
**bim2vcf** experiments severe error.
### Your environment
* version of jvarkit: 98f49441
* version of java:
openjdk 11 2018-09-25
OpenJDK Runtime Environment 18.9 …
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#### What data file(s) does this issue pertain to?
`cnv-controlfreec-tumor-only.tsv.gz`
#### What release are you using?
v13-v15
#### Put your question or report your issue here.
The st…
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### Description of feature
I have data consisting of several unrelated trios and several individuals. Is it possible to run the pipeline with just one samplesheet (where cases have different case_id)…
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Hi!
I am unable to download the CPTAC-3 SNV data:
- Code
```
query
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In this [example](https://github.com/uclahs-cds/package-iSubGen?tab=readme-ov-file#load-and-format-data), `csnvs` should be `snv`
In this [example](https://github.com/uclahs-cds/package-iSubGen?tab…
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Hi Ruolin,
I found that the numbers in the output.mutation_metrics.txt don't seem to be consistent with each other.
As seen in the image below, n_A_eval + n_C_eval + n_G_eval + n_T_eval is not equ…
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Hi, thanks for the great tool. When running metapop-1.0, I encounter the following error:
```
Rscript MetaPop.R -dir 0.9.microdiversity/0.1.metapop/0.1.bam/ \
-assem ttk3610.cleaned.fasta \
-ct …
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Sorry, this is not an issue, just a question regarding the difference between picard liftover and your tool.
I recently tried picard's liftover for lifting over from 37 to 38, and I came across t…
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**Describe the bug**
VarDict SVs once again end up in the SNV VCF files, making them hard to visualise for the user when loaded in Scout.
**To Reproduce**
Load e.g. case `novelbear` (or presumabl…
dnil updated
8 months ago