Moderator: Cyriac Kandoth
Cyriac Kandoth ♦ 4.6k
- Reputation:
- 4,610
- Status:
- Trusted
- Location:
- Memorial Sloan Kettering, New York, USA
- Website:
- https://www.linkedin.c...
- Twitter:
- icyreaction
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 week, 1 day ago
- Joined:
- 5 years, 1 month ago
- Email:
- c*******@gmail.com
I'm a computer scientist that studies the genetics of cancer in search of druggable targets, early diagnoses, and prevention. I intend to stick with this line of research till it becomes obsolete. In the meantime, there's no shortage of work to bring this science to the masses.
Posts by Cyriac Kandoth
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... For your final objective, you should not use vcf2maf. The "MAF" in vcf2maf refers to "Mutation Annotation Format", which was something unncessarily invented and confusingly named for cancer genetics. This possible confusion was already disambiguated in [the post](https://www.biostars.org/p/123822) t ...
written 22 days ago by
Cyriac Kandoth ♦ 4.6k
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... If you already have these [Phase 1 1000 genome VCFs](ftp://ftp.1000genomes.ebi.ac.uk:/vol1/ftp/phase1/analysis_results/integrated_call_sets) downloaded, then the Global Allele Frequency is within `AF` under the `INFO` column. The VCF format is complex, so don't try to write your own code to parse ou ...
written 22 days ago by
Cyriac Kandoth ♦ 4.6k
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... I see similar "vocabulary bubbles" in people who study cancer genetics (like me) vs people who spent their careers studying genetics of germline/mendelian diseases. Every research institute invents its own vocabulary. Clearly, we don't get out much. :) ...
written 22 days ago by
Cyriac Kandoth ♦ 4.6k
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Comment:
C: Karyotypically Ordered Hg19
... Anything within backticks are simply shell commands that run and return with their standard output for Perl to parse. So in this case, you just add one more argument to the Unix `cat` command. Like this - `cat $d/GL* $d/KI*`
Btw, I don't recommend using in-line Perl in a production workflow. Beside ...
written 7 months ago by
Cyriac Kandoth ♦ 4.6k
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Answer:
A: genome version in cbioportal
... Sorry that this isn't explicit on the portal. All variants in all studies use `GRCh37.p13` loci and alleles. The autosomes and sex chromosome sequences are equivalent to `hg19`, but the mitochondrial DNA sequence is newer. [Click here](https://www.biostars.org/p/119295/#119308) for details.
The eff ...
written 10 months ago by
Cyriac Kandoth ♦ 4.6k
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Comment:
C: RUN genome music (MuSiC2) error
... 1. What are the instructions you are following? Have you seen this: https://www.biostars.org/p/62793/
2. Does your system have docker installed? This will nearly obsolete the need for installation.
3. "zlib" is a popular development library, so it makes sense for a root user to install it system-wid ...
written 11 months ago by
Cyriac Kandoth ♦ 4.6k
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Comment:
C: TCGA CNV Files
... Can you create a new post for your question. And clarify it with an example of the normal samples you see listed as nocnv. ...
written 11 months ago by
Cyriac Kandoth ♦ 4.6k
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... Note that the lab has since released a [MuSiC2](https://github.com/ding-lab/MuSiC2), which is also [dockerized here](https://hub.docker.com/r/beifang/music). ...
written 11 months ago by
Cyriac Kandoth ♦ 4.6k
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... Thank you both. I've updated the tutorial to use the new URLs of the R tarballs. ...
written 11 months ago by
Cyriac Kandoth ♦ 4.6k
5
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... The standard 34 MAF columns [described here](https://wiki.nci.nih.gov/x/gwBwCw) don't include any pathogenicity prediction data, beyond `Variant_Classification`. But the various centers that generated these TCGA MAFs added their own columns, in no particular format or consistency. These include data ...
written 13 months ago by
Cyriac Kandoth ♦ 4.6k
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