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We use HaplotypeCaller and Strelka2 to call germline mutations, unlike somatic mutations where we use MuTect2 and Strelka2. However, the MuTect2 column is created when `vcf2maf.pl` is called (empty co…
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Refers to https://github.com/mskcc/vaporware/issues/101
--- The best approach would be to call blood normal vs. a curated pooled normal of young patients without any hematological malignancies. We …
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updates such as my recent effort to move everything to python3 take an amount of time that is super-linear with the amount of code.
We have a lot of un-used/little-used tools. I propose that we remove…
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Hello Folks,
Strelka2 is our go to caller for standard somatic variant calling. It works well down to about 5% AF. We'd like it to work with our ctDNA variant calling where the read depth exceeds…
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Hi, I am using oncokb-annotator to annotate somatic mutations from a large cohort of patient samples. I am aware that OncoKB database is regularly updated. I was wondering if there is a way of running…
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- Mutect2 calling
- From a combined VCF file with two genotypes {tumor, normal}, annotate the variants with SnpEff, and output a protein XML with those variations
- Adapt `Proteomics.VariantApplicat…
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For instance, in CKG, we have distinct mutations:
```
sequence variant:
represented_as: node
preferred_id: [clinically relevant, known, somatic]
label_in_input: [Clinically_relevant_variant, Kn…
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Sections 7 to 10 are a list of dot points and I would like to see the details added. A collaborator is considering using Infinium MethylationEPIC arrays for cutaneous squamous cell carcinoma. But, the…
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Hello,
I would like to use the pipeline to call somatic mutations from tumor-only RNAseq data. Would you mind to detail that how to generate the Panel of Normals?
Thanks,
Ya
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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…