User: poisonAlien
poisonAlien • 2.5k
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Cancer genomics
Posts by poisonAlien
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Comment:
C: TMB Tumor Mutation Burden
... I believe standard WXS capture sizes are around 50 mb. (eg; Agilent sure select) ...
written 5 months ago by
poisonAlien • 2.5k
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... I am not sure if I understand teh question correctly. But, you should look at one of those multi region WXS/WGS studies. Somatic mutation profile varies a lot within the bulk tumor based on biopsy site. So its pretty heterogeneous. ...
written 5 months ago by
poisonAlien • 2.5k
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... Its using Mutect2 under the hood for variant calling and doing LOT of filtering to remove possible FPs and gremline variants - which is GOOD. I think you should try it! ...
written 6 months ago by
poisonAlien • 2.5k
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... If you have only tumor samples, no matter how much of a sophisticated algorithm you use - there is always an uncertainty associated with the somatic status of an identified variant. Having said that, MuTect can still call somatic variants without gremline controls. But again you will have to be care ...
written 6 months ago by
poisonAlien • 2.5k
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... There are few other tools. DeconstructSigs estimates loading of known signatures for every sample in the cohort. If you are interested in de-novo you could try [EMu](http://www.sanger.ac.uk/science/tools/emu) and [Mutational Signature framework](https://www.mathworks.com/matlabcentral/fileexchange/3 ...
written 7 months ago by
poisonAlien • 2.5k
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... Try [Here](https://github.com/PoisonAlien/beadAnalyze) ...
written 7 months ago by
poisonAlien • 2.5k
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... Hi,
You're passing MAF object as an input for `SomInaClust_det` function. My guess is it requires MAF file as an input. May be try this and see...
```r
brca_Sominaclust <- SomInaClust_det(maf_brca, calculate_CDS = TRUE, convert_genenames_to_HGNC=FALSE)
``` ...
written 8 months ago by
poisonAlien • 2.5k
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418
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... Hi,
Whether a gene is a driver or not is usually done on large cohorts based on how frequently the gene is mutated. There are algorithms to identify such genes. How many cell lines do you have in your file ?
In case if you're only interested in a particular mutation,
- you will have to look at ...
written 10 months ago by
poisonAlien • 2.5k
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... They are Ensemble Gene IDs. See [here][1] for converting them to Gene symbols.
[1]: http://www.ensembl.org/Help/Faq?id=125 ...
written 10 months ago by
poisonAlien • 2.5k
1
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... > The "MAF" in vcf2maf refers to "Mutation Annotation Format", which was
> something unncessarily invented and confusingly named for cancer
> genetics.
So true! This also conflicts with [Multiple Alignment Format][1]
[1]: https://cgwb.nci.nih.gov/FAQ/FAQformat.html#format5 ...
written 11 months ago by
poisonAlien • 2.5k
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