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Hey,
Thanks for developing the SCmut tool. I am trying to use it on my own data, but my tumor- and normal- bulk bam file are all generated based on hg38. I try to use `gatk mutect2` to call somati…
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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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Hi,
I'm trying to use Pisces to call a tumour-only sample. I'm using the following command:
```shell
$ dotnet Pisces.dll -bam tumour.bam \
-CallMNVs false -g hs37d5 -gVCF false \
-i h…
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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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I want to detect the ctdna indel which frequency is ~1%(4000X), and I have tried the param --candidate-indel-input-vcf which have inclued the indel, but the strelka indel result still not reserve the…
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There'll be a new `SV_STATUS` field that'll indicate SOMATIC or GERMLINE, see [doc](https://docs.google.com/document/d/1kfih0P9gNrFoY_FfWl-x3cGOL98u7gh3T6I5ZU_6q14/edit). We should show this in the on…
inodb updated
9 months 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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Home Page:
- [x] Blurb (further detailed in about) (Slack Barry or Mike): needs text. Method, Assay, Glossary, etc
- [x] Change the blurb on front page from using bold to highlight the letters in …
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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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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…