Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller17k
Reputation:
17,460
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Location:
Washington University in St. Louis, MO
Website:
http://www.chrisamille...
Scholar ID:
Google Scholar Page
Last seen:
16 hours ago
Joined:
7 years 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 • 926 results • page 1 of 93 • next >
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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 days ago by Chris Miller17k
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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 18 days ago by Chris Miller17k
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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 Somatic Sniper has largely been superceded by a new generation of callers (Mutect, Strelka, etc) but is still useful in the niche case of having tumor contamination in your normal sample (very few other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 5 weeks ago by Chris Miller17k
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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 5 weeks ago by Chris Miller17k
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7 follow
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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 5 weeks ago by Chris Miller17k
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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 7 weeks ago by Chris Miller17k
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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 7 weeks ago by Chris Miller17k
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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 10 weeks ago by Chris Miller17k
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Comment: C: fastq.gz Error: Not in gzip format
... "file" should be a valid command on just about any *nix system. Did it output an error or what? ...
written 3 months ago by Chris Miller17k
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Comment: C: fastq.gz Error: Not in gzip format
... What OS are you using? ...
written 3 months ago by Chris Miller17k

Latest awards to Chris Miller

Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Popular Question 21 days ago, created a question with more than 1,000 views. For Importing A Large Number Of References From Text
Scholar 5 weeks 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 8 weeks ago, created an answer that was upvoted at least 5 times. For A: Aligning Reads To Specific Chromosome Using Bwa
Appreciated 8 weeks ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Appreciated 3 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Extract Base Based On Position From Bam File
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 3 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Aligning Reads To Specific Chromosome Using Bwa
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Hardware Suitable For Generic Nextgen Sequencing Processing?
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
Appreciated 6 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Appreciated 6 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Great Question 7 months ago, created a question with more than 5,000 views. For Bioinformatics "Cheat Sheet"
Scholar 7 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 8 months ago, created a post with more than 5 votes. For A: Difference Between Somatic And Germline Variant Calling?
Scholar 9 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Scholar 9 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome

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