Moderator: Chris Miller

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Chris Miller19k
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Location:
Washington University in St. Louis, MO
Website:
http://chrismiller.sci...
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Google Scholar Page
Last seen:
1 day, 16 hours ago
Joined:
8 years, 3 months ago
Email:
c***********@gmail.com

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 • 1,049 results • page 1 of 105 • next >
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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 13 days ago by Chris Miller19k
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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 22 days ago by Chris Miller19k
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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 24 days ago by Chris Miller19k
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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 26 days ago by Chris Miller19k
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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 26 days ago by Chris Miller19k
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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 4 weeks ago by Chris Miller19k
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Answer: A: Sciclone clonevol integration
... Yes, if clonevol doesn't come up with a valid consensus model, then it's impossible to plot that model. You should examine your results carefully to identify 1) artifactual calls that may result in clusters that are wrong (one class of reference-problem-induced FP tends to be at about 15% in every s ...
written 4 weeks ago by Chris Miller19k
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Answer: A: Can sciclone handle multiallelic variants?
... Sciclone was written to assume that each variant's chr:pos would be unique. The simple workaround for collisions like this is just to give the second variant a different chrom and pos. (i.e. chr99 999999999). The places actual coordinates are used are for matching up variants with the CN regions to ...
written 4 weeks ago by Chris Miller19k
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Comment: C: SciClone not numeric error
... You really should ask this as a top-level question, not buried in the comments of someone else's comment. Are your CN values log2? If so, then you need to set the appropriate "cnCallsAreLog2" parameter ...
written 4 weeks ago by Chris Miller19k
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Answer: A: somaticsniper VAF calclulation
... See: https://github.com/genome/somatic-sniper/issues/9 ...
written 4 weeks ago by Chris Miller19k

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Popular Question 7 weeks ago, created a question with more than 1,000 views. For Efficiently storing methylation data from BS-sequencing
Scholar 8 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
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Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
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Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 6 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Scholar 7 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
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