Moderator: Cyriac Kandoth
Cyriac Kandoth ♦ 5.3k
- Reputation:
- 5,320
- 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, 4 days ago
- Joined:
- 6 years, 11 months 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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Comment:
C: How to convert vcf to MAF ?
... It is not possible to convert VCF format to `multiple alignment format` because one represents variants and the other represents sequence alignments. VCFs can be converted to `mutation annotation format` because both represent variants. ...
written 4 months ago by
Cyriac Kandoth ♦ 5.3k
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Comment:
C: How to convert vcf to MAF ?
... Do not edit code to change the values of `$vep_path` and `$vep_data`. Use command-line arguments `--vep-path` and `--vep-data` instead. Please see more in documentation printed when using argument `--help`. ...
written 4 months ago by
Cyriac Kandoth ♦ 5.3k
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... hi. This has been answered at https://www.biostars.org/p/127955/ ...
written 12 months ago by
Cyriac Kandoth ♦ 5.3k
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... Yes, I keep it up to date with what's open/filled. You can also visit http://careers.mskcc.org and query for "Center for Molecular Oncology" ...
written 14 months ago by
Cyriac Kandoth ♦ 5.3k
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... The [CMO][1] is one of several [Collaborative Research Centers][2] at [MSKCC][3] that help researchers translate their work into real benefits for cancer patients and clinicians. To this end, we interface with investigators across MSKCC, understand their research/clinical questions, and design seque ...
written 21 months ago by
Cyriac Kandoth ♦ 5.3k
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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 23 months ago by
Cyriac Kandoth ♦ 5.3k
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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 23 months ago by
Cyriac Kandoth ♦ 5.3k
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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 23 months ago by
Cyriac Kandoth ♦ 5.3k
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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 2.4 years ago by
Cyriac Kandoth ♦ 5.3k
2
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1.3k
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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 2.7 years ago by
Cyriac Kandoth ♦ 5.3k
Latest awards to Cyriac Kandoth
Appreciated
11 months ago,
created a post with more than 5 votes.
For A: Where is the pathogenicity in TCGA MAF files?
Appreciated
11 months ago,
created a post with more than 5 votes.
For A: From TCGA to GDC (Genomic data commons)
Appreciated
11 months ago,
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For C: Working With Maf Files (Mutation Annotation Format) From The Tcga (The Cancer Ge
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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
Epic Question
12 months ago,
created a question with more than 10,000 views.
For Installation of the MuSiC suite on unsupported Linux distributions
Good Answer
16 months ago,
created an answer that was upvoted at least 5 times.
For A: TCGA CNV Files
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16 months ago,
created an answer that was upvoted at least 5 times.
For A: TCGA CNV Files
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19 months ago,
created a question with more than 1,000 views.
For Installation of the MuSiC suite on unsupported Linux distributions
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21 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
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For A: how can I get MAF stratified by subpopulation for ASW, or CEU and YRI
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For A: how can I get MAF stratified by subpopulation for ASW, or CEU and YRI
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For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
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For A: how can I get MAF stratified by subpopulation for ASW, or CEU and YRI
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For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
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2.7 years ago,
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For A: Tcga: "Tumor, Matched Normal" Vs. "Normal, Matched Tumor"
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For A: how can I get MAF stratified by subpopulation for ASW, or CEU and YRI
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For A: Selecting TCGA samples by barcode in CG Hub
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For Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
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For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
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For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
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For A: how can I get MAF stratified by subpopulation for ASW, or CEU and YRI
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3.0 years ago,
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For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
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For A: Music - Problems With Installing In Ubuntu And Where Do We Start With Loading In
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For Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
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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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