Moderator: Cyriac Kandoth

gravatar for Cyriac Kandoth
Cyriac Kandoth5.4k
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Location:
Memorial Sloan Kettering, New York, USA
Website:
https://www.linkedin.c...
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icyreaction
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Last seen:
2 hours ago
Joined:
7 years, 3 months ago
Email:
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I'm an engineer who studies the pathogenesis of genetic diseases like cancer. My specialty is to learn what biologists/clinicians do for a living, and help them do more with automation and user-interfaces.

Posts by Cyriac Kandoth

<prev • 262 results • page 1 of 27 • next >
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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 8 months ago by Cyriac Kandoth5.4k
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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 8 months ago by Cyriac Kandoth5.4k
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Comment: C: Does a no-normal pipeline exist for MuSiC?
... hi. This has been answered at https://www.biostars.org/p/127955/ ...
written 17 months ago by Cyriac Kandoth5.4k
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Comment: C: Open positions at the Center for Molecular Oncology, MSKCC, New York
... Yes, I try to keep it up to date with what's open/filled. You can also visit http://careers.mskcc.org and query for "CMO". ...
written 19 months ago by Cyriac Kandoth5.4k
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Job: Open positions at the Center for Molecular Oncology, MSKCC, New York
... The [CMO][1] is one of several [Collaborative Research Centers][2] at [MSKCC][3] with the mission to promote precision oncology through large-scale molecular profiling of tumors and correlation to clinical outcomes. This work informs the treatment strategies of oncologists at MSK, providing tangible ...
cancer python job sequencing R genetics written 2.2 years ago by Cyriac Kandoth5.4k
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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 2.3 years ago by Cyriac Kandoth5.4k
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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 2.3 years ago by Cyriac Kandoth5.4k
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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 2.3 years ago by Cyriac Kandoth5.4k
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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 2.8 years ago by Cyriac Kandoth5.4k
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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 3.1 years ago by Cyriac Kandoth5.4k

Latest awards to Cyriac Kandoth

Teacher 4 weeks 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 15 months ago, created a post with more than 5 votes. For A: Where is the pathogenicity in TCGA MAF files?
Appreciated 15 months ago, created a post with more than 5 votes. For A: From TCGA to GDC (Genomic data commons)
Teacher 16 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 17 months ago, created a question with more than 10,000 views. For Installation of the MuSiC suite on unsupported Linux distributions
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: TCGA CNV Files
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: TCGA CNV Files
Popular Question 24 months ago, created a question with more than 1,000 views. For Installation of the MuSiC suite on unsupported Linux distributions
Appreciated 2.2 years 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 2.4 years 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 2.5 years 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 2.5 years 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 2.6 years 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 2.8 years 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 3.0 years ago, created an answer that was upvoted at least 5 times. For A: Tcga: "Tumor, Matched Normal" Vs. "Normal, Matched Tumor"
Appreciated 3.1 years 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 3.1 years ago, created an answer that has been accepted. For A: Selecting TCGA samples by barcode in CG Hub
Teacher 3.2 years 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 3.2 years 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 3.2 years 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 3.4 years 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 3.4 years 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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