Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller17k
Reputation:
17,390
Status:
Trusted
Location:
Washington University in St. Louis, MO
Website:
http://www.chrisamille...
Scholar ID:
Google Scholar Page
Last seen:
7 hours ago
Joined:
6 years, 11 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 • 924 results • page 1 of 93 • next >
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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 Somatic Sniper has largely been superceded by a new generation of callers (Mutect, Strelka, etc) but is still useful in the niche case of having tumor contamination in your normal sample (very few other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 12 days 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 12 days 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 13 days 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 22 days 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 22 days 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 6 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 9 weeks ago by Chris Miller17k
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Comment: C: fastq.gz Error: Not in gzip format
... What OS are you using? ...
written 9 weeks ago by Chris Miller17k
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Answer: A: fastq.gz Error: Not in gzip format
... Well, start by making sure that they're gzipped files and not just errantly named: $ file tmp.gz tmp.gz: gzip compressed data,was "tmp", from Unix, last modified: Tue Dec 13 13:12:02 2016, max compression Also try opening it without unzipping less file.gz If the output comes back as ...
written 9 weeks ago by Chris Miller17k
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Answer: A: BAM to FASTQ
... Samtools is not the right tool for this job. Try bedtools bamtofastq (after name-sorting your bam): https://bedtools.readthedocs.io/en/latest/content/tools/bamtofastq.html ...
written 9 weeks ago by Chris Miller17k

Latest awards to Chris Miller

Scholar 11 days ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Appreciated 13 days ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Appreciated 4 weeks ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: Aligning Reads To Specific Chromosome Using Bwa
Appreciated 9 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: Extract Base Based On Position From Bam File
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 9 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 3 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: Hardware Suitable For Generic Nextgen Sequencing Processing?
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Aligning Reads To Specific Chromosome Using Bwa
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
Appreciated 5 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Appreciated 5 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Great Question 6 months ago, created a question with more than 5,000 views. For Bioinformatics "Cheat Sheet"
Scholar 6 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 7 months ago, created a post with more than 5 votes. For A: Difference Between Somatic And Germline Variant Calling?
Scholar 8 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Scholar 8 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome

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