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When I was running ScanNeo2, several samples encountered errors during the VEP annotation process, specifically for the main task of SNVs. The following error occurred for all of them.
localrule ann…
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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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CIViC (Clinical Interpretation of Variants in Cancer) is an open-access, community-driven resource for the clinical interpretation of cancer variants. To enhance Scout’s functionality for somatic vari…
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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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Hi,
Thanks for developing this awesome tool.
I'd like to call somatic structural variants (SVs) using paired tumor and normal samples. However, cuteSV can only process one sample at a time.
I…
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Issue by @MaxUlysse, moved from SciLifeLab#666
- [ ] [ExpansionHunter](https://github.com/Illumina/ExpansionHunter) for estimating repeat sizes
- [ ] [QDNAseq](https://github.com/ccagc/QDNAseq) CN…
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Currenty, the user can only classify a variant according to the ACMG guidelines. However, for somatic variants it would be good to also have support for the [ClinGen-CGC-VICC Guidelines](https://pubme…
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## Background
List of ids for every widget and its column that cant be disabled
Format below:
widget - column to be fixed
## Tasks
**Target profile**
- [ ] Known Drugs - Drug
- [ ] Safety - Safe…
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I'm interested in tracing previously identified somatic mutation for each single cell. am wondering if the souporcell_merged_sorted_vcf.vcf.gz contains only germline variants or it also contains somat…
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Hi there,
The way we usually run bioinformatics software in our centre is to use Docker containers from the Biocontainers project, via singularity/apptainer.
The Biocontainers project automatica…