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Hi!
I would like to know if it is possible to use Smurf with tumor-only mode.
I know VarScan and Strelka2 can`t work with tumor-only, so I would have only the VCFs for freebayes, GATK and VarDict. I…
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Currently only tumor-normal VCFs are supported.
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This is because the human gene has a preferred label of `tp53`, while the mouse gene has a preferred label of `trp53`. It is therefore being sorted below all the other genes that have a preferred labe…
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Hi, I'm new to snakemake, and have no idea of submitting Scanneo2 jobs to HPC. Any instructions would be very helpful! Thanks!
Regards,
Xiao
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We are using vembrane on a multi-sample VCF files and got the following error message:
```
vembrane only supports records with one alternative allele.
Please split multi-allelic records first, fo…
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thanks a lot
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As an example, (I hope that this Scout-link will persist): https://scout-stage.scilifelab.se/cust087/F0049453/sv/variants/8e2113f40646b16473f9a12af4e57e0b
This is one of the variants that we're loo…
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Hi,
We have been running multiple SV callers on high coverage data (275x tumor / 156x normal). We have observed that SvABA seems to be making quite a few SV calls that are about 500bp in size and o…
mej54 updated
5 years ago
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GREIN is a fantastic tool for exploring RNA-seq data, and I greatly appreciate it. However, there appears to be an issue where certain datasets include only 20 samples each, which is not consistent wi…
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## FEATURE REQUEST
### Inspiration
Biological samples are defined by the metadata associated with them. If two samples are identical in every way except the name, they are very likely errant d…