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Hi,
We have some tools that expect to see allele depths in FORMAT column (ie A,C,G,T or AU,CU,GU,TU) and TIR/TAR for indels. Would be great if there was a way to get these in the vcf output.
Tha…
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Hello,
does Bamsurgeon has and option to spike in mutations with a low VAF avoiding allelic bias?
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### Type
Game behaviour
### Bug description
I was editing a local beatmap that I had made on an existing beatmap set, and I had added two extra difficulties and went to change the hp drain. I did n…
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### Description
In conjunction with developing a PR for changing filters and settings for variants called with Manta, I reached out to one of our customers to ask if they were aware of any WGS cases …
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Hello
I am trying to use clonevol in my data, I have been succeed in the function infer.clonal.models , then I faced some errors when I used the function convert.consensus.tree.clone.to.branch , th…
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Hello,
I would like to report a bug for this newly introduced feature: [#2746](https://github.com/cBioPortal/cbioportal-frontend/pull/2746)
Everything works smoothly apart of the VAF plot shows …
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### Need
As a clinician I want to be able to detect all true somatic variants, but currently in WGS-tumor-only cases we are filtering out all somatic variants with a VAF of 1 with a bcftools filter…
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Maybe I am misunderstanding something, but when I try to use hyphens "-" in commented LaTeX text, a "-" is added to the beginning of each visual line. The same thing happens with "*". In contrast, oth…
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Hello!
I have tried using vcflat on a deepvariant vcf, however it crashes:
singularity exec vcflat_latest.sif python -m vcflat -i P10051_107.clean.dedup.bam.vcf -o P10051_107.clean.dedup.bam.vcf.c…
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I have enjoyed using Clair3 (clair3-arm64) for examining natural variants at the whole-genome level. However, I've recently noticed some irregularities that likely need correction.
Specifically, I …