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### Need
As a clinician interpreting cases with a significant risk of equal presence of somatic variants in the matched normal, I want the ability to adjust the somatic in normal frequency when doi…
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Hi,
I used clairs(v0.4) to call somatic SNV/InDel(tumor/normal paired), but the PASS variants number is ~6w. Is it normal?
Compare to deepsomatic, the somatic SNV/InDel number is ~1.7w.
Do you …
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### Need
As a geneticst, despite not having a matching normal sample for germline filtering, I want to be sure that all somatic variants I am interpreting are true somatic variants, and not germlin…
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I have assembled a single haplotype and aligned it to the hg38 reference genome. Then, I used SVision to call structural variants (SVs). When I called SVs using each haplotype separately, both haploty…
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we will need to disambiguate between variants (and perhaps any geno partonomy) that are germline vs somatic.
how should these be represented? should there be classes for "germline variant" "somati…
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I was testing `pipeline_v6.0` branch of `nf-core/oncoanalyser` in targeted mode. `purple` failed as below only for some of the samples. Same [issue](https://github.com/nf-core/oncoanalyser/issues/100)…
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Will possibly update once project-specific sample purity is determined but tentative additions (may relax or make stricter)
Filters to add for FilterMutectCalls:
```
FilterMutectCalls \
…
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Hi,
I'm experimenting with running COMPASS (using CNVs) with multiple samples (3 samples), where the cells then come from different runs with MissionBio. A problem is that they got sequenced at dif…
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I run strelka2 version 2.9.10 with paired normal-tumor somatic mode, and got an site which indicated that it should be LOH type.
1 241663871 . G A . LowEVS SOMA…
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Hi, we installed Monopogen using git clone:
git clone https://github.com/KChen-lab/Monopogen.git
cd Monopogen
pip install -e .
path="~/Monopogen"
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${pat…