Moderator: Chris Miller

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Chris Miller18k
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Location:
Washington University in St. Louis, MO
Website:
http://www.chrisamille...
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7 years, 1 month 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 • 938 results • page 2 of 94 • next >
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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 22 days 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 23 days 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 5 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 6 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 Somatic Sniper has largely been superceded by a new generation of callers (Mutect, Strelka, etc) but is still useful in the niche case of having tumor contamination in your normal sample (very few other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 9 weeks ago by Chris Miller18k
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Comment: C: Whole Genome Sequences somatic MAF files at TCGA
... Are you talking about AML specifically, or WGS in general from TCGA projects? ...
written 9 weeks ago by Chris Miller18k
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Job: Cancer Analysis Group Leader - McDonnell Genome Institute - Washington University in St. Louis
... https://facultyopportunities.wustl.edu/apply/Posting/Detail/1010106 We're seeking a talented, ambitious individual to lead a small team of cancer analysts here at the McDonnell Genome Institute. The job entails analyzing and interpreting genomic data from a variety of cancer genomics projects, both ...
analysis job wustl cancer written 9 weeks ago by Chris Miller18k
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Answer: A: Bam-readcounts min-base-quality not giving expected output
... answered here: https://github.com/genome/bam-readcount/issues/37 ...
written 11 weeks ago by Chris Miller18k
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Answer: A: Regions to Exclude and useSexChromosome questions
... > What exactly should be the content of the 'Regions to Exclude' file? Yes, The usual use is to exclude CN-neutral LOH regions. You should actually call LOH regions in a similar manner to calling copy-number calls. I don't have a script handy at the moment, but the short version is, run Varscan ...
written 11 weeks ago by Chris Miller18k
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Answer: A: Correcting for tumor purity in tumor evolution analysis
... Most experienced cancer genomic folks will agree that pathology estimates of tumor content are often inaccurate. If the genomic sequencing tells you that the VAFs max out at 20, then your sample is likely 40% tumor (and 60% non tumor - normal contamination). That said, there may be cases where you ...
written 3 months ago by Chris Miller18k

Latest awards to Chris Miller

Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Good Answer 2 days ago, created an answer that was upvoted at least 5 times. For A: Aligning Reads To Specific Chromosome Using Bwa
Appreciated 2 days ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 19 days ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Importing A Large Number Of References From Text
Scholar 9 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Appreciated 9 weeks ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Appreciated 12 weeks ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer 12 weeks ago, created an answer that was upvoted at least 5 times. For A: Aligning Reads To Specific Chromosome Using Bwa
Appreciated 4 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Extract Base Based On Position From Bam File
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 4 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Aligning Reads To Specific Chromosome Using Bwa
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Hardware Suitable For Generic Nextgen Sequencing Processing?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Aligning Reads To Specific Chromosome Using Bwa
Appreciated 7 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Appreciated 7 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Great Question 8 months ago, created a question with more than 5,000 views. For Bioinformatics "Cheat Sheet"

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