Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller18k
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Location:
Washington University in St. Louis, MO
Website:
http://www.chrisamille...
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Google Scholar Page
Last seen:
1 day, 13 hours ago
Joined:
7 years, 2 months ago
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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 • 943 results • page 2 of 95 • next >
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Comment: C: Bam-readcount output empty from certain regions (RNA seq bams)
... The details are fuzzy in my mind at the moment, but I suspect there is a difference between sites with coverage, where all reads fail quality checks (0) vs sites without any coverage (not output). ...
written 5 weeks ago by Chris Miller18k
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Answer: A: Bam-readcount output empty from certain regions (RNA seq bams)
... Yes, if there is no coverage of your variant, then bam-readcount will return nothing for that site. This includes sites for which there are no reads that meet your filtering criteria. ...
written 5 weeks ago by Chris Miller18k
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Answer: A: bam-readcount tool: output zero coverage bases
... You are correct that bam-readcount does not output zero-coverage bases. It requires a little post-processing to add those back in. (such as what's done here https://github.com/genome/genome/blob/master/lib/perl/Genome/Model/Tools/Analysis/Coverage/BamReadcount.pm) ...
written 5 weeks ago by Chris Miller18k
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Answer: A: How to plot mutation hotspot according to mutation counts
... There are several R packages and online tools, but I'd probably start with http://www.cbioportal.org/mutation_mapper.jsp ...
written 5 weeks ago by Chris Miller18k
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Comment: C: What is Copy Number Variation(CNV) and Alteration(CNA)
... One more comment - the example you give, of `GCGATGA` appearing more than once, is usually referred to as an indel. Generally speaking, SV/CNVs are bigger than 1kb, indels are smaller than 100bp, and there's also a weird middle range where the terms are often mixed. ...
written 8 weeks ago by Chris Miller18k
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Comment: C: What is Copy Number Variation(CNV) and Alteration(CNA)
... Yes, this is correct. In TCGA, for whatever reason, the nomenclature used was CNV. They're used interchangeably enough that you're pretty much always going to have to look at the context to figure out which one is being discussed. ...
written 8 weeks ago by Chris Miller18k
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Answer: A: What is Copy Number Variation(CNV) and Alteration(CNA)
... Typically, CNV refers to germline events, which are variants in the population. CNA usually refers to somatic events, like those found in tumors. They are sometimes used interchangeably. Confusingly, this is different from single-nucleotide events, which are SNPs (germline events in the population ...
written 8 weeks ago by Chris Miller18k
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Answer: A: Deciding on a Variant Caller
... Any modern caller should be "good enough" for most high-VAF calls in relatively pure samples (70% counts as relatively pure, in my book). When you need low-VAF data or are worried about tricky regions, my preferred approach is to run several callers, merge the calls, then do some post-filtering. S ...
written 10 weeks ago by Chris Miller18k
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Comment: C: bam-readcount error bam_header_read
... Have you verified that your bam looks legit with `samtools view sample1_sorted.bam | less` ...
written 11 weeks ago by Chris Miller18k
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Answer: A: SomaticSniper VS Varscan2
... It just depends on what you're doing. Somatic Sniper has largely been superceded by a new generation of callers (Mutect, Strelka, etc) but is still useful in the niche case of having tumor contamination in your normal sample (very few other callers are designed to handle this case). In general, VarS ...
written 3 months ago by Chris Miller18k

Latest awards to Chris Miller

Scholar 23 days ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Scholar 24 days ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
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Scholar 29 days ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Appreciated 5 weeks ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Aligning Reads To Specific Chromosome Using Bwa
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
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Appreciated 7 weeks ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
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Popular Question 12 weeks ago, created a question with more than 1,000 views. For Importing A Large Number Of References From Text
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Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 5 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
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Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Aligning Reads To Specific Chromosome Using Bwa
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Hardware Suitable For Generic Nextgen Sequencing Processing?
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