-
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…
-
### 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…
-
Will possibly update once project-specific sample purity is determined but tentative additions (may relax or make stricter)
Filters to add for FilterMutectCalls:
```
FilterMutectCalls \
…
-
Greetings,
I have a germline deletion candidate in a tumor/normal experiment that looks like the following going into 'varlociraptor preprocess variants'
`X 115190645 . GGGGG…
-
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…
-
Hello,
I run Muse sump with -D option and provide a dbSNP VCF file. What exactly does -D do?
If there are somatic variants at dbSNP positions (in other words; germline match normal is homozygous…
-
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…
-
Following on from https://github.com/umccr-illumina/dragen/issues/53
vc-enable-phasing is currently running by default in the somatic pipeline and generating FORMAT/PS tags
To enable combing SNVs …
-
Hi,
It would be nice to have a link to the COSMIC database for the variants listed in the inherited analysis pipeline in Scout as it is in the somatic analysis pipeline today. Germline/mosaic varia…
-
Hi!
Is it possible to filter the cancer variants by 'Qual' to, for example, obtain only 'PASS' variants or filter out cancer-germline variants? Alternatively, can the 'Qual' field be sorted so that '…