Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller20k
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Location:
Washington University in St. Louis, MO
Website:
http://chrismiller.sci...
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2 hours ago
Joined:
8 years, 4 months ago
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I work in the Genome Institute at Washington University in St. Louis, where I lead a group that develops and applies computational tools to give us insight into the origins and progression of cancer.

Posts by Chris Miller

<prev • 1,053 results • page 1 of 106 • next >
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Answer: A: high frequency SNPs (and other variations) after subtracting blood variants from
... If you're trying to call somatic variants, you should use a somatic variant caller (Such as Mutect, Strelka, or VarScan). The results will be different than if you simply compare tumor SNPs to normal SNPs, as there are statistical assumptions that are very different between the two models. ...
written 13 hours ago by Chris Miller20k
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Answer: A: Should bioinformaticians learn the scientific names of plants and animals?
... Almost certainly no. Beyond "Homo sapiens" and "Mus Musculus", there are probably only two or three I'd recognize. You'll pick up domain specific knowledge like that by diffusion from whatever project you're on, but a calculated study of them is probably not a good use of your time. ...
written 7 days ago by Chris Miller20k
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Answer: A: How to distinguish methylated cytosine and unmethylathed cytosine?
... You've just answered your own question. At each C/T in the genome, you'll see a mix of methylated (preserved base) and unmethylated (changed base) reads. The methylation fraction for a site is the methylated count over the total reads at that base. ...
written 20 days ago by Chris Miller20k
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Answer: A: Neoantigen prediction Tools
... I've helped to develop [pVACtools](https://github.com/griffithlab/pVACtools) along with some very talented people from the Griffith lab here at WUSTL. It works well [Vaxrank](https://www.biorxiv.org/content/early/2017/05/27/142919) is another, from the Hammerbacher lab ...
written 20 days ago by Chris Miller20k
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Comment: C: Work With Dnacopy (Bioconductor) And Varscan Copynumber Results
... Yes. In most cases, the probes or regions are small enough, that treating them as point estimates is fine. ...
written 5 weeks ago by Chris Miller20k
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Answer: A: Clonal evolution for samples with no common CNV
... You're going to have to provide more information, starting with exactly what the error message was. I strongly suspect that the message was "ERROR: no sites are copy number neutral and have adequate depth in all samples", which means you need to look at your inputs carefully. Did your points meet ...
written 6 weeks ago by Chris Miller20k
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Comment: C: Sciclone took too long
... Tumor only means that you will almost certainly not be able to remove all germline mutations. The isown paper will provide some useful guidelines for how you can minimize them though. https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-017-0446-9 ...
written 6 weeks ago by Chris Miller20k
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Comment: C: SciClone: Why cluster in non-CN neutral region considering it infers only on CN
... Yep, you've got it. Just look at the 2 copy plot for clustering. There's also an option to show just the CN2 regions in the plotting command. ...
written 7 weeks ago by Chris Miller20k
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Answer: A: SciClone: Why cluster in non-CN neutral region considering it infers only on CN
... > Then why do I see clusters on non-CN neutral region (1 copy and 3 copies)? They're plotted by default in a 1d view (in the appropriate row), but not utilized for clustering. I'd need more information on exactly what your inputs and outputs are to offer more help. ...
written 7 weeks ago by Chris Miller20k
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Answer: A: Sciclone took too long
... Are your 19k sites from exome or WGS? If the former, I suspect that something has gone horribly wrong with your mutation calling. In a decade of working on tumors, I've only seen a handful of MMR/POLE deficient cases with that kind of mutational burden in an exome. Sciclone will also take a long ti ...
written 7 weeks ago by Chris Miller20k

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Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
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Popular Question 10 weeks ago, created a question with more than 1,000 views. For Efficiently storing methylation data from BS-sequencing
Scholar 11 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
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