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thanks for making this software calling the complex variant, this super all others.
but I found another problem, for tumor-only, even for paired, has high FP.
these days I also test a paired stand…
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Hello,
When trying to run SmartRNASeqCaller using docker and nextflow, I get the following error at the final step. Not sure if the error is coming from the Rscript command or the split_vcf.py comm…
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https://beta.monarchinitiative.org/variant/ClinVarVariant:44739#disease
We should show the diseases associated with this paricular variant (available from ClinVar)
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I do not see vardict saying it support germline calling, but in this paper "Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data", it use vardict for variant calling
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I am running somatic structural variant calling with 3 callers - lumpy, manta and cnvkit on paired tumor-normal exomeSeq samples. When bcbio finishes running, I don't get an ensemble vcf like I see fo…
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Per planning meeting 6/26, we will limit annotation of the germline MAF to:
- ClinVar ~_(VEP annotation does add ClinVar but we might need to investigate whether it's sufficient: https://useast.ens…
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Getting the error msg below from vep using the latest devel version of bcbio-nextgen.
```MSG: ERROR: Can't use --most_severe and --biotype together```
```
[2019-05-07T07:19Z] Ensembl variant e…
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thanksa for this useful software.
after readoing this. I have some puzzles.
because the somatic examples does not give tumor-only mode, just give this
> If a normal sample is not present the canc…
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Hi,
I am having problems running Sarek with the latest version of nextflow (19.07). The error I get is:
```
Command error:
.command.run: line 196: uname: command not found
.command.run: l…