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Hi
thanks for putting together these great learning resources.
Would it be possible to add the correct answers and some explanations to the exercises at the end of [intro lesson 00](https://gith…
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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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I was looking for the mutation data through TCGA portal using TCGAbiolinks and I have realized that sample size are not the same.
for instance TCGA-OV case TCGA data portal shows 419 cases, however…
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This issue is for integrating and visualizing clonal hematopoiesis mutations into cBioPortal. From [Ptashkin et al, 2018](https://www.ncbi.nlm.nih.gov/pubmed/29872864): "Clonal hematopoiesis (CH) is t…
jjgao updated
4 years ago
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When calculating TMB for all public studies, we found `cscc_hgsc_bcm_2014` with unexpected high TMB scores (see this PR: https://github.com/cBioPortal/datahub/pull/1428). Altho in MAF all mutations ar…
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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 have tumor-only WGS, consisting of nodulous and tumorous tissue.
Your program is very interesting because filtering germline mutations in these samples have seemed very difficult and almost imp…
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Hello,
I would like create a dataset for benchmark somatic variant caller with your software. Thanks for this clear documentation and your well-designed tool ! I just don't fully understand the gen…
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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…