Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller19k
Reputation:
18,600
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Location:
Washington University in St. Louis, MO
Website:
http://www.chrisamille...
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Google Scholar Page
Last seen:
21 hours ago
Joined:
7 years, 8 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 • 991 results • page 1 of 100 • next >
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Comment: C: Stochastic modelling and differential expression analysis
... This post does not ask an answerable question. If you are, for example, looking for specific resources or techniques, that could be a valid question, but you're going to have to provide a lot more information to get good answers. For this reason we have closed your question. This allows us to keep ...
written 6 days ago by Chris Miller19k
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Comment: C: Bias During Exome Capture For Cnv Analysis
... I noticed an upvote on this, and thought I'd add that this comment is rather dated, and there are fairly good methods for exome CN calling now ...
written 9 days ago by Chris Miller19k
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Comment: C: NGS on cancer tumor
... Agreed, with the addendum that I believe it's fair game here to ask questions about terminology or how sequencing data is processed and analyzed. Doctors are busy and patients seeking to understand results isn't a bad thing, as long as we're careful not to cross the line into making treatment recomm ...
written 9 days ago by Chris Miller19k
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Answer: A: SciClone: Which Variant to Which Clone
... Yes, that is exactly the point of SciClone. :) That said, there are always some caveats. - Variants in CN-altered regions are more difficult to place because of VAF-shifts and will require some manual intervention. - the possibility of "cryptic" subclones is always there. That is, multiple subc ...
written 9 days ago by Chris Miller19k
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Comment: C: NGS on cancer tumor
... The description you provide isn't internally consistent. If a heterozygous mutation is in every cell of the tumor, then the VAF/MAF will be at 50% of the tumor purity. Think about a pure population of 100 cells. Each cell has 2 copies of each gene, but only one that's mutated (for a het event). Thi ...
written 9 days ago by Chris Miller19k
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Answer: A: NGS on cancer tumor
... 1) Your ability to infer this depends greatly on the depth of sequencing. It helps to picture each VAF with error bars on it, that grow smaller as your depth increases. In 30x sequence, 35% is absolutely not significantly different from 20-28%. In a 500x tumor, it probably is. 2) Without seeing y ...
written 10 days ago by Chris Miller19k
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Comment: C: NGS on cancer tumor
... > It's rare that a mutation in tumor is homozygous. That's emphatically not true, as chromosomal deletions (or copy-number neutral LOH) lead to homozygosity quite often in tumors. ...
written 10 days ago by Chris Miller19k
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Answer: A: Survey/Vote: If you could double the speed of any three commandline tools, which
... Here's another one: Bam-readcount, which is fairly fast, until you try to get counts/info for 3M SNPs from a WGS bam file https://github.com/genome/bam-readcount ...
written 13 days ago by Chris Miller19k
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Answer: A: Survey/Vote: If you could double the speed of any three commandline tools, which
... In the interest of offering useful leads: 1) The neural networks used for MHC Class I and II epitope binding prediction. (sadly, most are not open source - see http://tools.iedb.org/mhci/ ) 2) Variant annotation with [VEP](https://github.com/Ensembl/ensembl-vep). It's an amazing tool, but is relat ...
written 14 days ago by Chris Miller19k
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Comment: C: Survey/Vote: If you could double the speed of any three commandline tools, which
... One thing to consider is that for lots of operations on "big data" sets, disk I/O is the limiting factor (or even network speed), so speeding up the code may not help! ...
written 14 days ago by Chris Miller19k

Latest awards to Chris Miller

Scholar 9 days ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Commentator 13 days ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Good Answer 15 days ago, created an answer that was upvoted at least 5 times. For A: Any Experiences/Solutions For Problems With The Last R Update?
Appreciated 15 days ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 16 days ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: Can Anyone Suggest Me A Script Based Pipeline For Exome Sequencing With Paired E
Scholar 28 days ago, created an answer that has been accepted. For A: Can Anyone Suggest Me A Script Based Pipeline For Exome Sequencing With Paired E
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Why Should I Use Galaxy ?
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 8 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: Any Experiences/Solutions For Problems With The Last R Update?
Scholar 11 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: Difference Between Somatic And Germline Variant Calling?
Popular Question 3 months ago, created a question with more than 1,000 views. For Cancer Genomics/Genomic Medicine - The Genome Institute at WUSTL
Popular Question 3 months ago, created a question with more than 1,000 views. For Will Picard MarkDuplicates also un-mark duplicates?
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?
Epic Question 5 months ago, created a question with more than 10,000 views. For Bioinformatics "Cheat Sheet"
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
Popular Question 5 months ago, created a question with more than 1,000 views. For Exon Array Analysis Tools
Popular Question 5 months ago, created a question with more than 1,000 views. For Exon Array Analysis Tools
Scholar 5 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome

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