Moderator: Cyriac Kandoth
Cyriac Kandoth ♦ 5.4k
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- Location:
- Memorial Sloan Kettering, New York, USA
- Website:
- https://www.linkedin.c...
- Twitter:
- icyreaction
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- Google Scholar Page
- Last seen:
- 2 hours ago
- Joined:
- 7 years, 3 months ago
- Email:
- c*******@gmail.com
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
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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 Kandoth ♦ 5.4k
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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 Kandoth ♦ 5.4k
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... hi. This has been answered at https://www.biostars.org/p/127955/ ...
written 17 months ago by
Cyriac Kandoth ♦ 5.4k
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... 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 Kandoth ♦ 5.4k
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... 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 ...
written 2.2 years ago by
Cyriac Kandoth ♦ 5.4k
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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 2.3 years ago by
Cyriac Kandoth ♦ 5.4k
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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 2.3 years ago by
Cyriac Kandoth ♦ 5.4k
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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 2.3 years ago by
Cyriac Kandoth ♦ 5.4k
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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 Kandoth ♦ 5.4k
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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 Kandoth ♦ 5.4k
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For C: Working With Maf Files (Mutation Annotation Format) From The Tcga (The Cancer Ge
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