Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller18k
Reputation:
17,790
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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
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 • 943 results • page 1 of 95 • next >
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Answer: A: The meaning of VAF and LOH in sciclone
... VAF = variant allele frequency, expressed as a percentage between 0 and 100. The most typical use case for Regions to exclude is the case of copy number neutral loss of heterozygosity: that is, an area that has copy number 2 but has the same alleles twice due to uniparental disomy. ...
written 18 days ago by Chris Miller18k
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Answer: A: How can I make VEP recognize header lines in my VCF?
... Update - this doesn't seem to happen on my laptop's more recent install of VEP (version 87 vs version 86). I guess it's either a version issue or a somehow screwy install. I'm going to go ahead and mark this as the best answer for now, as an upgrade seems like it will solve the problem. If anyone ...
written 23 days ago by Chris Miller18k
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Comment: C: How can I make VEP recognize header lines in my VCF?
... Sadly, that's not the issue. I'm editing the post above to make the VCF even simpler and make the FORMAT lines match up 100% with the fields - the same warning and header recognition issue persists. ...
written 23 days ago by Chris Miller18k
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How can I make VEP recognize header lines in my VCF?
... Here's a massively simplified VCF file with one line: ##fileformat=VCFv4.1 ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT M_CJ-R878H_AML1-R878H_AML1 1 3329234 . G T 36.8 . TIER=1 GT 1/1 If I run VEP on it like ...
vcf annotation vep written 23 days ago by Chris Miller18k
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Answer: A: My translated A.A seq longer than my original Nucleotide seq!! Could someone exp
... The search is returning the entire protein's sequence, just part of which matches your nucleotide sequence. If you translate your sequence using something like this site: http://web.expasy.org/translate/ You'll see that part of the sequence (starting with VSFANSFT...) is present in the aa sequence ...
written 29 days ago by Chris Miller18k
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Answer: A: Generate column names on the fly R
... You'll probably want to look into the `scan()` function, and use the `nlines` parameter. https://stat.ethz.ch/R-manual/R-devel/library/base/html/scan.html Off the top of my head, I might do something like: 1) read in the first 100 lines of the file with scan, keep only those that match my comment ...
written 5 weeks ago by Chris Miller18k
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Comment: C: StackExchange/Area51 bioinformatics is back
... It's fair, and I don't expect Istvan to single-handedly shoulder the load. It would be great to have a development roadmap that's transparent to the community, as well as recruitment of contributors (paid or volunteer), if the platform is going to continue to grow. Right now, things seem to have st ...
written 5 weeks ago by Chris Miller18k
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Comment: C: StackExchange/Area51 bioinformatics is back
... This is a good point - Tutorials and the Job Board, in particular are really nice. ...
written 5 weeks ago by Chris Miller18k
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Answer: A: StackExchange/Area51 bioinformatics is back
... I can see why lousy search, difficult UI, etc are frustrating to some folks. BioStars has the community and knowledgebase, but there doesn't seem to be a clear plan to improve the site, and reach feature parity with SE. Istvan, would you care to weigh in on those topics? More than anything, I just ...
written 5 weeks ago by Chris Miller18k
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Answer: A: bam-readcount values are higher than Mutect results
... Many callers do some filtering of reads first (by base quality, by mapping quality, maybe even local realignment) and report only counts from reads that pass. bam-readcount, by default, outputs "raw" counts. You may or may not be able to mimic those Mutect settings with bam-readcount parameters. ...
written 5 weeks 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
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
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
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
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
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Importing A Large Number Of References From Text
Scholar 3 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Appreciated 3 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Appreciated 4 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
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?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Extract Base Based On Position From Bam File
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
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
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?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack

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