Moderator: Cyriac Kandoth

gravatar for Cyriac Kandoth
Cyriac Kandoth4.6k
Reputation:
4,610
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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

<prev • 257 results • page 1 of 26 • next >
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Answer: A: Installing ensembl 86 VEP and vcf2maf and getting SNP MAFs
... 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 Kandoth4.6k
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Answer: A: Getting 1000 Genomes phase one MAF values
... 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 Kandoth4.6k
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Comment: C: Getting 1000 Genomes phase one MAF values
... 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 Kandoth4.6k
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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 Kandoth4.6k
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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 Kandoth4.6k
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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 Kandoth4.6k
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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 Kandoth4.6k
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Comment: C: Installation of the MuSiC suite on unsupported Linux distributions
... 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 Kandoth4.6k
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Comment: C: Installation of the MuSiC suite on unsupported Linux distributions
... Thank you both. I've updated the tutorial to use the new URLs of the R tarballs. ...
written 11 months ago by Cyriac Kandoth4.6k
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Answer: A: Where is the pathogenicity in TCGA MAF files?
... 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 Kandoth4.6k

Latest awards to Cyriac Kandoth

Appreciated 8 weeks ago, created a post with more than 5 votes. For A: how can I get MAF stratified by subpopulation for ASW, or CEU and YRI
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
Appreciated 3 months ago, created a post with more than 5 votes. For A: how can I get MAF stratified by subpopulation for ASW, or CEU and YRI
Appreciated 4 months ago, created a post with more than 5 votes. For A: how can I get MAF stratified by subpopulation for ASW, or CEU and YRI
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Tcga: "Tumor, Matched Normal" Vs. "Normal, Matched Tumor"
Appreciated 10 months ago, created a post with more than 5 votes. For A: how can I get MAF stratified by subpopulation for ASW, or CEU and YRI
Scholar 10 months ago, created an answer that has been accepted. For A: Selecting TCGA samples by barcode in CG Hub
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
Appreciated 12 months ago, created a post with more than 5 votes. For A: how can I get MAF stratified by subpopulation for ASW, or CEU and YRI
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
Popular Question 17 months ago, created a question with more than 1,000 views. For Installation of the MuSiC suite on unsupported Linux distributions
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
Scholar 18 months ago, created an answer that has been accepted. For A: how can I get MAF stratified by subpopulation for ASW, or CEU and YRI
Appreciated 20 months ago, created a post with more than 5 votes. For A: how can I get MAF stratified by subpopulation for ASW, or CEU and YRI
Popular Question 21 months ago, created a question with more than 1,000 views. For Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In

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